Campylobacter is a Gram-negative, microaerophilic bacterium that can be transmitted to humans through the consumption of raw milk, causing foodborne diseases. This study investigated the prevalence of pathogenic species in raw milk and local sheep cheese using molecular methods in Farsan city of Chaharmahal and Bakhtiari provinces in 2013. Twenty samples of raw milk and 20 samples of local sheep cheese were randomly collected from collection centers and traditional milk and dairy stores. All the samples were transferred to the laboratory as soon as possible in sterile containers under suitable cold chain conditions. DNA extraction from the samples was done using a commercial kit, and then polymerase chain reaction (PCR) was performed using appropriate primers to identify Campylobacter. Of the 20 samples of raw milk, 2 (10%) were contaminated with the bacteria, and none of the 20 samples of local cheese were infected. According to the results of the present study and the presence of the mentioned bacteria in milk, it is necessary to observe hygiene principles in the dairy industry, to process and use sufficient heat to destroy the bacteria in raw milk, and to use fast and accurate methods to identify this bacterium.