Mycotic mastitis due to Candida is increasing and the identification of Candida species is crucial in choosing the ideal antifungal drugs. Identification of Candida to species level is essential as many non-albicans Candida developed drug resistance against antifungal agents. A total of 138 milk samples (24, 15, 46 and 53 from goats, sheep, buffaloes and cows, respectively) were streaked on plain plates of SDA and incubated. CHROM agar was used to differentiate Candida isolates. Mycological examination revealed the presence of yeast in 8.3, 6.7, 32.6 and 47.2% milk samples of goats, sheep, buffaloes and cows, respectively. The total isolation percent of yeast in all milk samples was 31.2%. Species identification of Candida in the present work using both CHROM agar and the bio-typing assay (API 20 C AUX) revealed the highest presence of Candida albicans (11.6%) followed C. glabrata (5.8%), C. tropicalis (5.1%) and C. krusei (2.9%). Multiplex PCR gave two different sized PCR products specific for every tested Candida isolates separately. It was concluded that phenotypic and biochemical assays are time-consuming and exposed to misdiagnosis. Whereas multiplex PCR is a genotypic-based technique that permits the identification of species that is difficult to be identified conventionally because of their abnormal morphology or biochemical features and also this assay is simple, easy and time saving so it is recommended to be implemented in clinical laboratories.