Air-borne fungi are responsible for producing several diseases in fruits and vegetables and allergic disorders in human beings. An aeromycological study of fruit and vegetable markets of Barpeta town and Sonkuchi Colony of Barpeta district, Assam was conducted from January to December, 2018 to analyze different fungal species exhibit in the environment using Culture Plate exposure method. A total of 30 different fungal species belonging to 19 genera were isolated from Barpeta town fruit and vegetable market, while 27 species belonging to 19 genera were from Sonkuchi Colony market. A total of 3609 and 2963 fungal spores were isolated from Barpeta town and Sonkuchi Colony market respectively throughout the year. The most and least dominating fungal species in Barpeta town market were recorded to be Aspergillus niger and Drechslera sp. respectively, while in the Sonkuchi Colony market, they were Cladosporium herbarum and Botrytis sp. respectively. The number and types of fungal species varied between the two markets. The maximum number of fungal spores was recorded in the month of August and the minimum was in January 2018. The growth of the fungal population is influenced by season and meteorological factors, which play a vital part in the composition and concentrations of aeromycoflora. There was a definite relationship found between the fungal spores and the markets. So, proper management of the waste is needed in the markets by the Municipality Board. The vegetable-market solid wastes can be used for preparing vermicomposting and biogas for minimizing environmental pollution and maintaining sustainable management.