Alright so—over the course of the original trilogy and its anime adaptation we see magatamas in the following colors:

Yellow

Blue

Green

Pink

And lavender

And the breakdown for who has what color is as follows:

Maya always wears yellow

Mia wears yellow before she abdicates her claim to the Master’s seat, then switches to blue

Pearl always wears blue

Misty is seen wearing yellow in flashbacks, and the magatama Morgan is holding in a certain scene in episode 15 (I’m pretty sure it’s 15) of the anime is also yellow

The one Phoenix has is green

The big wooden one in Hazakura Temple is also green

Bikini wears pink

Iris wears lavender

So then, what in the heck does all that mean? Here are my thoughts.

Yellow is the main family’s color—or, a little more specifically, the color of magatama worn by people who are in the direct line of succession. The people we see wear this color are Mia, Maya, and Misty, and Mia stops wearing it after she abdicates.

Blue is the branch family’s color, or rather, it’s worn by close relatives of the main family who aren’t in the direct line of succession. Pearl exclusively wears blue, and Mia wears blue after she abdicates (and is therefore no longer in the direct line of succession).

Green allows its holder to see Psyche-Locks. We never see anyone do this with any magatama other than the green one Maya gives to Phoenix—specifically, we as the player never see any hint of Psyche-Locks while we’re playing as Mia, whose magatama is a different color, and in case 3-2 Maya (who has a magatama herself) is surprised to learn that Phoenix’s can do that. Plus, the big wooden one in Hazakura Temple is green as well, implying some significance to green; especially since it would’ve made a lot of sense for it to be either yellow (the main family’s color) or…

Pink, which is worn by the temple nuns. In more detail, as far as I can tell this color is worn by members of the Kurain School who have little to no spiritual power but still play an important role, as it’s the color Bikini wears and while she doesn’t seem to be able to channel herself, she runs Hazakura Temple and it’s a requirement that either she or another nun supervises any spiritual training that happens there.

And that brings us to lavender, our final color. This is a fun one—I’m pretty sure it’s less a color with its own significance than it is a subtle hint about Iris’ true identity! Lavender is approximately the color you’d get by mixing temple nun pink and branch family blue!