Four different intertidal estuarine sediments had distinct yeast communities. One-hundred-ninety-three yeast isolates were classified in 47 species, with 34 of these in the genus Candida. Candida tropicalis was the only ascomycetous species isolated from all four sites. Other opportunistic pathogens including Candida glabrata, Candida guilliermondii, Candida parapsilosis and Candida krusei were present, especially at the more polluted sites. Pichia species were also frequent isolates with Pichia membranaefaciens, and its anamorph, Candida valida, and other phenotypically similar low assimilation profile species the most frequent. Kluyveromyces aestuarii was prevalent at the only site with well established mangrove vegetation, but not present at the other sites. The sediment yeast communities were distinct from each other, but more similar to each other than to the yeast communities of other ecosystems in the same geographic region.