Yoghurt is the most popular type of fermented milk in Egypt and around the world, and its sensory attributes, have a large effect on consumer acceptability and it is nutritiously balanced food containing most the nutrients gift in milk but in a more assailable form. A total of 120 random samples of plain yoghurt (Companies and Dairy shops) and fruit yoghurt were purchased from different dairy shops and supermarkets from different places from Cairo Governorate. Phenotype-based ways for identifying yeast particularly Candida species are often difficult, time-consuming and not enough to identify most yeast species. Molecular biological techniques provide a useful alternative approach to identify yeast. The polymerase chain reaction was applied for identification of some isolated yeast especially Candida species, Yarrowia, Trichosporn, and Rhodotorula. PCR product of the isolate by ITS regions subjected to restriction enzymes ( MspI). The internal transcribed gene regions were digested with restriction enzymes MspI (Thermo scientific ) generated bans corresponded to the predicted size (330 – 600 bp).