Cheese production by native starter cultures instead of commercial ones is beneficial in respect of higher quality, nutrient content, immunogenicity and having beneficial microorganism. The objective of the presented study was molecular identifying of microorganism and exploring its active ingredients in native cheese. MRS and M17 media were used to culture bacteria in 15, 37 and 45°c for 24, 48 and 72 hours and then morphologic and biochemical tests were used to identifying the species. Predominant species were detected using 16S rRNA and gene sequencing. Active ingredients and fatty acid profile was studied by GC lactobacili, lactococci and enterococci were identified as the predominant bacteria. Acid palmitic had the highest concentration among the saturated fatty acid, with 42.47%, and acid meristic and acid lauric acid were next with the 13.22% and 3.9% concentration respectively, among the unsaturated fatty acids.