To investigate the DNA fingerprinting of Candida zeylanoides (C. zeylanoides) strains and the correlation between genotyping and antifungal susceptibility of C. zeylanoides. Paper discs containing nystatin, ketoconazole, fluconazole, Zataria multiflora (Z. multiflora) and Pulicaria gnaphalodes (P. gnaphalodes) essential oils were used in the disc diffusion method to evaluate the in vitro activity of the antifungal agents by measuring the mean diameter of inhibition around the discs. Yeast isolates were characterized by randomly amplified polymorphic DNA (RAPD) analysis using two different primers. The mean inhibition zones were calculated 36.1 ± 2.2mm for ketoconazole, 25.3 ± 2.0mm for nystatin and 14.9 ± 1.4mm for fluconazole. Z. multiflora essential oil revealed a 58.6 ± 2.6mm mean zone of inhibition while P. gnaphalodes showed a 36.7 ± 1.8mm zone of inhibition against all isolates tested. A total of 14 strains of C. zeylanoides were divided into three types, 1 was genotype A strain, 2 genotype B strains and 11 genotype C strains. Strain of genotype A was significantly more susceptible to ketoconazole and nystatin than fluconazole (P<0.05). Strains of genotype B were more susceptible to ketoconazole than other antifungal agents (P>0.05). Strains of genotype C were significantly more susceptible to ketoconazole than fluconazole and nystatin (P<0.05). There was a significant correlation between C. zeylanoides genotypes and antifungal susceptibility (P < 0.05). We concluded that all C. zeylanoides genotypes were susceptible to nystatin and Z. multiflora essential oil. The correlation between antifungal susceptibility and C. zeylanoides genotype may be of potential therapeutic significance and larger studies are needed to prove this finding.