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Ancillary Justice by Ann Leckie*

Once, Breq was Justice of Toren, a starship whose artificial intelligence linked through the minds of a multitude of human ancillary bodies. Now, there is only Breq, a lone soldier seeking vengeance after a horrific act of betrayal cost her everything. As Breq gets closer to her goal, the conquering empire she once served begins to destabilize from the inside, and Breq herself has to question her priorities as new loyalties arise. Features female-as-neutral worldbuilding, as well as singular characters existing throughout many bodies.

Note: my favorite from this series is Translation State, which gets really weird about gender and sexuality and stands fairly well on its own, go read it!

The Black Tides of Heaven by Neon Yang

Novella series. In a world where children choose their gender when they're ready, twins Mokoya and Akeha once swore never to pick. But as they grow older, the two find themselves drawn in different directions, both in terms of gender and in what they want from their lives. Rebellion is brewing, and the twins' mother is looking to use them to her whims to retain power. Akeha, unwilling to be her pawn, resorts to leaving home and falling in with the rebels.

The Unraveling by Benjamin Rosenbaum*

On a distant planet in a distant future, everyone has multiple bodies that can be customized however they want, cybernetics have abolished nearly all privacy, and the gender binary is no longer about man or woman. Instead, there's vail and staid, for which biological sex is irrelevant. Fift should be focusing on the obligations of a staid, but is distracted by budding feelings for Shria, forbidden due to Shria being a vail. When their complicated relationship unexpectedly becomes the center of a growing revolution, they will both have to decide where their priorities lie.

Dawn by Octavia E. Butler*

After a devastating war leaves humanity on the brink of extinction, survivor Lilith finds herself waking up naked and alone in a strange room. She’s been rescued by the Oankali, who have arrived just in time to save the human race. But there’s a price to survival, and it might be humanity itself. Absolutely fucked up I love it I once had to drop the book mid read to stare at the ceiling and exclaim in horror at what was going on. Includes darker examinations of agency and consent, so enter with caution.

The Javelin Program by Derin Edala

Dr Aspen Greaves expected to be woken from decades of cryo sleep on humanity’s first deep space colony, but instead finds themself alone on a spaceship still years away from its goal. Surrounded by mysteries on a barely functioning ship, Aspen must make sure the still sleeping crew reach their new home, while also dealing with the many secrets hidden behind the Javelin Program. Nonbinary and aromantic lead, based on a society and norms very far removed from ours.

Gideon the Ninth by Tamsyn Muir*

Gideon, raised as a swordswoman by unfriendly nuns, would rather run away and make her own life, but her services are needed. The Reverend Daughter, Gideon’s childhood nemesis, has been invited to a trial to win a place as an immortal by the Emperor’s side, and she’s in need of a bodyguard. Listen, if you’re on tumblr I probably don’t need to explain this book to you. Trust me when I say it’s exactly as good as people claim. Humorous and spooky but also absolutely gut wrenching and clever with a lot of political commentary. There are also, indeed, lesbian necromancers in space.

Too Like the Lightning by Ada Palmer

Centuries in the future, humanity has deliberately engineered society to be as utopian as possible, politically, socially, sexually, religiously. But things begin to crumble as the shadow of impending war looms. Written in an enlightenment style and featuring questions of human nature and whether it’s possible to change it, and what price we’re prepared to pay for peace, this book is simultaneously very heavy and very funny, and written in a very unique style. While still human, the society presented often feels starkly alien.

Walking Practice by Dolki Min

Having crashed their space ship, a shapeshifting alien finds themself trapped on Earth. Suffering from isolation and loneliness, they have settled into a routine to survive. Using online dating services, they take on the shape of human men and women to hunt humans for food. Strange, gross, and gender weird, Walking Practice is a unique take on gender from a wholly alien perspective.

The Stars are Legion by Kameron Hurley

Zan wakes without memory, a passenger aboard one of the living world-ships of Legion, a fleet of decaying generations ships. Told she’s the salvation meant to free them from the fleet, Zan is flung head first into a brutal and bloody conflict. This book fucked me up when I read it. It’s weird, it’s gross, there’s So Much Viscera, there are literally no men, it has living spaceships and biotech but in the most horrific way imaginable, where humans are nothing but part of an ecosystem that cares little for their well-being. It’s an experience but not necessarily a pleasant one.

All Systems Red by Martha Wells*

After having hacked its own governor module, SecUnit uses its small amount of new freedom to secretly download and watch as much media it can between doing its job guarding humans. But when the scientists it’s been charged with keeping safe come under attack, it must make a choice about whether to continue keeping its freedom secret or risk it all to save them. The series features both novellas and full length novels, and balances humor with scathing social critique. There's also an excellent tv adaptation!

Drinking Sapphire Wine by Tanith Lee

Four-BEE is a utopian city, in which humans have no responsibilities, are cared for by machines, and few acts cause true consequences as even death has been conquered. Able to change bodies and gender nearly at will, living lives of luxury and hedonism, everything should be perfect; yet the narrator finds him/herself dissatisfied with his/her life. After an impulsive decision leads him/her to break one of the only remaining taboos, he/she is exiled from Four-BEE into the wholly uninhabited desert wilderness outside.

The Cloud Roads by Martha Wells

Moon doesn't know what he is. Having lost his family young he lives on the move, shifting shape to hide his true form. The only ones similar to him he's ever encountered are the vicious, bloodthirsty Fell, but he knows he cannot be one of them. When chance leads to a meeting with someone like him, he hopes his days of loneliness are over. But his new people stand against a dangerous enemy, and not all of them welcome Moon's help. Featuring a world with not a single human in sight, The Cloud Roads makes for a unique perspective.

When the Angels Left the Old Country by Sacha Lamb*

The angel Uriel and the demon Little Ash have been friends for centuries, living and studying together in a small Jewish community in Europe. But times are changing, and many of the community have left for a new life across the sea. When one of these emigrants go missing, Uriel and Little Ash decide to leave their peaceful life to go find and, if needed, save her. While set in our own past rather than a fictional world/time like other titles on this list, the relationships and identities of the two main characters often break our ideas of gender as well as platonic/romantic.

The Summer Prince by Alaya Dawn Johnson*

Young adult. Young artist June Costa lives in Palmares Tres, a beautiful, matriarchal city relying heavily on tradition, one of which is the Summer King. The most recent Summer King is Enki, a bold boy and fellow artist. With him at her side, June seeks to finally find fame and recognition through her art, breaking through the generational divide of her home. But growing close to Enki is dangerous, because he, like all Summer Kings, is destined to die. Set in a world in which bisexuality and polyamory are largely the norm.

Dreamsnake by Vonda N. McIntyre*

In a future ravaged by disaster, Snake is a traveling healer who uses the venom of her snakes to concoct medicines for all imaginable ills. The most valuable of them all is her dreamsnake, an alien creature whose bite can grant a painless death. When circumstances cause her to lose her dreamsnake, she must embark on a dangerous journey to obtain a new one so she can continue her work. Set in a world where polyamory and bisexuality are largely the norm.

Shadow Man by Melissa Scott

As an effect of an FTL drug, intersex births increased, resulting in five separate genders among humans: men, women, mems, fems, and herms. But on the planet Hara, people cling to the old two gender system, forcing intersex individuals to pick one of the two and generally refusing to recognize their existence and needs. As conflict on the planet broils, Warreven, a Haran advocate and herm, and Tatian, an off-worlder, find themselves dragged into a struggle for equality.

Leech by Hiron Ennes*

Unbeknownst to humanity, a sentient hive mind has taken over the entire medical profession to ensure the health of their host species. One of their doctors is sent to an isolated location where they’re cut off from the rest of the hive mind, only to realize they’re faced with a rivaling parasitic entity. Leech hands you only just enough information to get by, and whether its historical fantasy, an alternate timeline, or futuristic post apocalypse is hard to determine. It’s spooky and weird and wildly creative, and does some neat things with gender, because what does gender even mean when you're a hive mind bacteria inhabiting countless bodies?

Axiom's End by Lindsay Ellis

It’s 2007, and a leak has just confirmed that the US has reached alien contact. Cora wants nothing to do with it, but as her absent father is the whistleblower who dropped the news the media won’t leave her alone. Even worse, she soon finds herself meeting and being stalked by the alien presence itself as it tries to remain in hiding - and discovering that there is a much larger threat on the horizon. Features aliens with very different ideas of gender and relationships than humans, and a central focus is how a relationship between one of them and a human would look like.

Ammonite by Nicola Griffith

Centuries ago, the first settlement on the planet Jeep was hit by tragedy: a virus killed off all men, leaving behind a society of only women. Now, the planet has been rediscovered, its inhabitants having long forgotten about the rest of humanity. Anthropologist Marghe Taishan is sent to test out a potential vaccine. If the vaccine succeeds, Jeep and its people would no longer be in forced quarantine, but it would also open them up to exploitation.

Ethan of Athos by Lois McMaster Bujold

For Dr. Ethan Urquhart living on Athos, delivering babies looks a little different: they are "born" from uterine replicators, as Athos is a planet populated entirely by men. But now they're running out of the ovarian cultures that allow them to reproduce. To replace them, Ethan is one of the first of his people to be sent off planet into the wider universe - where there are women, rumored to be an evil and corruptive force.

The Left Hand of Darkness by Ursula K. Le Guin

Genly Ai is an emissary sent to the planet of Winter, meant to help facilitate Winter’s inclusion in a growing intergalactic civilization. But he’s unprepared for Winter’s citizens, who spend much of their time genderless or switching between genders, making for a culture wildly different from what Genly is used to.

Meet Me in Another Life by Catriona Silvey*

Thora and Santi are strangers, brought together by a coincidence and torn apart just as abruptly when tragedy strikes. But this is neither the first nor the last time they meet - again and again they encounter each other, as friends, lovers, enemies, family, every time recognizing in each other a familiarity no one else carries. But with every new life, a mysterious danger grows ever closer, forcing them to find out the truth of their connection. This is a puzzle-box of a story that goes some entirely unexpected places in a very wild ride, featuring a bisexual co-lead and a very hard to define main relationship.

A Door Into Ocean by Joan Slonczewski

On the moon Shora live the Sharers, a nation of women who reproduce via parthenogenesis and have developed highly advanced biological sciences. Leading wholly pacifist lives, the Sharers are threatened when humans from another planet come across their world and decide to develop it, no matter what the Sharers themselves think. The Sharer society is openly sapphic, though the main romance is m/f.

Dust by Elizabeth Bear

In a dying spaceship, orbiting an equally dying sun, noblewoman Perceval awaits her own gruesome death. Having been captured by an opposing house, her wings severed and life forfeit, Perceval’s execution is imminent - until a young servant charged with her care proves to be Perceval’s long lost sister. To stop a war between houses likely to doom them all, the two flee together across a crumbling, dangerous spaceship. At its core waits Jacob Dust, god and angel, all that remains of what the ship once was. And he wants Perceval. Sapphic and asexual characters, however be prepared for kinda fucked up relationships.

Halfway Human by Carolyn Ives Gilman*

When Val, expert in alien cultures, gets called in to help handle the young Tedla after a suicide attempt, she is let in on a secret decades in the making. Tedla is neither male nor female, an asexual person from an isolated planet where a genderless class of 'blands' are exploited as a work force. As knowledge of Tedla's presence begins to spread, so does the attention of various parties wanting to use it for their own ends, including its old masters. As Val works to unravel the history of how Tedla came to leave its world, the pressure builds - what is to become of Tedla? Content warning for themes such as suicidal ideation, slavery, and child sexual abuse.

Moonstar Odyssey by David Gerrold

On the planet of Satlik, humanity have been changed: children are born genderless, and have the ability to choose between male and female during puberty. As a child coming of age, young Jobe finds herself having a hard time choosing what she wants to be, a decision coming into shadow as global disaster looms near. Novella length, focused as much on building up the history and lore of Satlik as it is on the coming of age story. Also an early example of female pronouns being used as default and neutral!

Venus Plus X by Theodore Sturgeon*

Charlie Johns is just your average guy, so when he suddenly finds himself pulled into the strange, utopian future of Ledom, he's shocked. In Ledom, gender is a thing of the past, as is hunger and war. Confused and wanting to return home, Charlie Johns is promised that he will be returned, but first the people of Ledom want him to tour their society. Charlie Johns agrees, but the more he learns and the better things seem, the more suspicion grows: why is he really here? Published in 1960, Venus Plus X is frankly astoundingly progressive about the topic of gender.

Trouble on Triton by Samuel R. Delany

On the moon Triton hundreds of years in the future, life looks a little different from our world. The only place yet to be drawn into a war spanning the entire rest of the solar system, society on Titan is in many ways a utopia, where everyone can live however they want, no matter how strange their ideals. Yet despite this, martian immigrant Bron Helstron isn't happy. Unable to build meaningful relationships or figure out what he actually wants out of life, Bron is prepared to all but turn himself inside out to figure things out. Strange, surreal, and a bit out there, I'd recommend this if you want a story with a fairly loose plot and prose that will scramble your brain. Not a personal favorite, but an impressive work.

Every Day by David Levithan

Young adult. A is neither boy nor girl - in fact, A doesn't have a body of their own. Every day they wake up inhabiting a stranger's body, and spend a single day living their life before waking up as someone else the next day. They try to be respectful of their hosts' lives, not making decisions they wouldn't themselves make, but after meeting and falling for Rhiannon, the girlfriend of one of their hosts, things begin to change as A begins pursuing their own wants.

Woman on the Edge of Time by Marge Piercy