Thirty yeast isolates belonging to the genera Kodamaea and Suhomyces were isolated from mushrooms and associated drosophilids collected in a Brazilian Amazonian rainforest biome. Analyses of the sequences of the intergenic spacer region and the D1/D2 domains of the large subunit rRNA gene showed that these isolates represent two distinct species. The first, represented by ten isolates, is phylogenetically related to Kodamaea plutei and Kodamaea lidongshanica based on the sequences of the D1/D2 domains. The name Kodamaea schenbergiae f.a., sp. nov. (Holotype CBS 18628T; MycoBank MB855624) is proposed to accommodate the species. The second species was represented by 20 isolates (13 isolates from drosophilids and 7 from mushrooms). This novel species is phylogenetically related to Suhomyces bolitotheri, Suhomyces rilaensis and Suhomyces choctaworum. The name Suhomyces schwaniae f.a., sp. nov. (Holotype CBS 18800T; MycoBank MB855625) is proposed to accommodate the species. Both novel species did not produce asci or evidence of conjugation when cultured individually or in pairs. The isolation of these yeasts associated with mushrooms and drosophilids in the Amazonian biome suggests that these substrates are the habitat of both species.