Thirty six samples of raw milk were collected from three different farms located in Merida, Yucatan, Mexico and seventy two samples of soft cheese were manufactured from thirty six samples of raw milk and thirty six samples of pasteurized milk from the previous collected raw milk during May 2013 to April 2014. The first and second farm located at Faculty of Veterinary Medicine and Animal Science, Autonomous University of Yucatan (FMVZ/UADY) used two different production regimes; intensive silvopastoral system (ISS) and traditional system (TS). The third farm in Kampepen under (ISS). The collected raw milk samples were divided into three portions, one portion of raw milk and two portions for soft cheese manufacture from (raw and pasteurized milk) for PCR screening. PCR screening was performed for one hundred and eight samples to detect four types of the most dangerous foodborne pathogens (Escherichia coli O157:H7, Salmonella enterica serovar Typhimurium, Staphylococcus aureus and Listeria monocytogenes). PCR results showed that almost samples were negative for all tested pathogens except six samples (5.56%); 3 samples of raw milk and other 3 samples of soft cheese manufactured from this raw milk under traditional system which were positive for Staphylococcus aureus.