The microbiology of Kasseri cheese, a Protected Designation of Origin (PDO) cheese of pasta-filata type was studied in order to identify the dominant species and strains that may contribute to the maturation process. Chemical composition and microbiological quality of Kasseri cheese samples from two different dairies during the maturation was studied at 0, 7, 25, 60 and 90 days of the maturation. Lactic acid bacteria and Enterococcus spp. were found to be the dominant microflora in fresh cheese. P. pentosaceous and P. acidilactici, E. hirae, E. faecium, E. durans and E. gallinarium, together with facultatively heterofermentative lactobacilli were found to be the dominant microflora. Since these strains are dominating the microflora of Kasseri cheese during maturation, the enzymic system need to be further studied in order to select the proper strains for adjunct culture in Kasseri cheese.