Many traditional products such as cheese obtain their flavor intensity from non-starter lactic acid bacteria (NSLAB), which are not part of the normal starter flora but develop in the product, particularly during ripening, therefore it was decided to identify this group of bacteria from Iranian Lighvan cheese, made from raw ewe’s milk as it is by far the most popular Iranian cheese amongst consumers. Ten grams of cheese samples (in triplicates) were homogenized in a stomacher and using microbiological analysis for the isolated bacteria, it was noted that NSLAB formed a large part of the lactic flora at 4 months of ripening. The colonies were randomly picked from plates with 30-300 colonies for further studies. Isolates were phenotypically characterized by their ability to ferment different carbohydrates. Accordingly, they were classified into 3 predominant genera : Lactobacillus, Lactosphaera and Enterococcus (48, 39 and 13 % respectively). In case of Lactobacillus isolates close similarities to species L. plantarum and L.casei were observed. Classification in species level did not perform on Lactosphaera isolates, because there is a little information about this genus. All isolates of Enterococcus were identified as E. faecium. Due to the importance of Enterococcus in developing unique taste and flavor of the Lighvan cheese, molecular analysis was only performed on this species. By using specific primers for the structural enterocin A gene, the bacteriocin structural gene was found in 21 isolates out of 30 selected isolates. The presence of this gene in the wild E. faecium indicates that they might be used as industrial starter cultures to guarantee the safety of traditional characteristics of this kind of products.