The yeasts present during the ripening process of ewes' and goats' cheeses produced in a small traditional dairy in Mediterranean Spain were isolated and identified. Five hundred and thirty strains pertaining to eleven yeast species representing eight genera were identified using molecular methods. Debaryomyces hansenii was the yeast species most frequently isolated in all cheeses. Other yeast species commonly found in dairy products were present at the first maturing weeks. Two yeast species Trichosporon coremiiforme and Trichosporon domesticum have been reported in cheeses for the first time, and Meyerozyma guilliermondii has been newly isolated from goats' cheeses. Yeast species composition changed greatly along the process; although, D. hansenii dominated at the end of ripening in all cheeses. Most yeast isolates were able to hydrolyze casein and fatty acid esters. One hundred and eighty seven D. hansenii isolates were genotyped by PCR amplification of M13 satellites and an UPGMA dendrogram was constructed. The majority of isolates were grouped in 5 clusters while 7 profiles were represented by 1-3 isolates. These results demonstrate the genetic heterogeneity present in D. hansenii strains isolated from raw milk cheeses.