The recent change in the epidemiology of Candidiasis with emergence of non albicans species as the predominant agents is of serious concern globally. Speciation ofis very important since many of these species are associated with resistance to the common antifungal agents and often lead to treatment failures. The existing conventional methods for speciation are time consuming and tedious. We attempt to evaluate the performance of the four phenotypic methods for speciation of with molecular method.This observational study was conducted on all the clinically significant isolates of species obtained from various specimens for a period of 2 years. Speciation was done by phenotypic methods which include conventional germ tube test, chromogenic medium (HiCrome agar), corn meal agar and automated method-Vitek-2 system. Molecular speciation was done by multiplex polymerase chain reaction (PCR). Performance of phenotypic methods is evaluated with results of PCR as gold standard. During the study period, a total of 80 isolates of species from various clinical samples were enrolled in the study. Molecular speciation identified 25 (31.25%) which was the most common species, followed by 23 (28.75%), 13 (16.25%), 12 (15%), 4 (5%), 2 (2.5%) and one (1.25%). Comparing with molecular method, the sensitivity and specificity of chromogenic medium, corn meal agar and Vitek-2 compact system was found to be 91.25% and 100%; 83.75% and 100% and both 100% respectively.Overall non albicans spp predominated in the present study. Among the various phenotypic methods studied performance of HiCrome agar was very good and has the advantage of speciation directly from samples where as that of Vitek 2 Compact was excellent and but requires pure growth. Conventional methods failed to identify many species.