Koozeh cheese is an Iranian dairy product in rural areas, it is necessary to consider the microbial contamination in this supply.This study evaluates microbial contamination in Koozeh cheese by molecular tools.S. aureus and its enterotoxins including type A and type B were identified by biochemical and polymerase chain reaction (PCR) and molecular typing was done by RAPD (Random Amplification of Polymorphic DNA) method. A total of 42 sheeps and cows Koozeh cheese samples were collected from random market in the cities and the surrounding villages.71.42% of samples were contaminated with Staphylococcus spp. and in 50% of isolates, S. aureus specific coagulase gene "coa" was detected. High-level contamination was observed in 7.14% of samples. The SEA or SEB enterotoxins were produced in 42.84% of isolates. No clonal relationship was observed by molecular approach.The obtained results indicate a high level of microbial contamination in Koozeh cheese. Half of isolates were enterotoxin producer and had high diversity and no clonal relationship. Long processing and manipulation are involved in contamination. Improvement in hygiene, training local manufactures of Koozeh cheese, control of products for possible contamination and developing new protocols is needed to decrement of S. aureus contamination in Koozeh Cheese products.