In three different dairies (A, B and C) located in Peloponess region (Southern Greece), traditional Feta cheese trials took place February to March using mixtures of sheep's and goat's milk. Only small variations in the evolution of microbial groups were observed during the whole ripening period. The main groups, such as thermophilic cocci, mesophilic lactococci, thermophilic lactobacilli, nonstarter lactic acid bacteria (NSLAB), presumptive Leuconostoc, enterococci and micrococci, reached their highest levels during the first 16 days, and then declined approximately 1–2 log units until the end of ripening. The remaining groups investigated, comprising yeasts, coliforms and Escherichia coli, were highest at day 4. The yeasts remained constant, while coliforms and E. coli decreased sharply and were not detectable after 120 days of ripening. A number of 146 isolates (dairy A) taken from all stages of the manufacturing and ripening process were purified and studied. Lactobacillus plantarum (58/146) and isolates of related species Lactobacillus pentosus and Lactobacillus paraplantarum (16/146) were the most common microorganisms found during cheese ripening. Streptococcus thermophilus (23/146) and Lactobacillus delbrueckii subsp. bulgaricus (20/146) were detected in high levels up to 20 days, and then gradually reduced. Enterococcus faecium (29/146) was found in all manufacturing and ripening stages.