The aim of this work was to identify the predominant yeast species present at different anatomical sites in healthy dogs and to determine their in vitro antimicrobial susceptibility using a broth microdilution assay. Samples were collected from the preputial, vaginal, oral and perianal mucosae and the isolates cultured were identified according to their morphological characteristics and biochemical profile. Malassezia pachydermatis was the most commonly isolated yeast, followed by Candida parapsilosis, Candida tropicalis, Candida albicans, Saccharomyces cerevisiae and Rhodotorula spp. Minimum inhibitory concentrations of the azole derivatives ketoconazole, itraconazole and fluconazole against Candida spp. were 0.03-16 microg/mL, 0.06 to >16 microg/mL and 0.5-64 microg/mL, respectively and Candida isolates were sensitive to caspofungin and amphotericin B. Although all isolates of M. pachydermatis were sensitive to itraconazole, fluconazole, ketoconazole and amphotericin B, they were found to be resistant to caspofungin. The study has highlighted that Candida spp., M. pachydermatis, S. cerevisiae and Rhodotorula spp. are part of the normal canine surface microbiota and some of these organisms exhibit in vitro resistance to commonly used antimicrobials.