Over the past decade, the occurrence of milk-borne infections caused by Shiga toxin-producing Escherichia coli (STEC) and Salmonella enterica serovar Typhimurium (S. Typhimurium) has adversely affected consumer health and the milk industry. We aimed to detect and genotype the strains of E. coli and S. Typhimurium isolated from cow and goat milks using two genotyping tools, BOX-PCR and ERIC-PCR. A total of 200 cow and goat milk samples were collected from the dairy farms in Southern Sarawak, Malaysia. First, E. coli and Salmonella spp. detected in the samples were characterized using PCRs to identify pathogenic strains, STEC and S. Typhimurium. Next, the bacterial strains were genotyped using ERIC-PCR and BOX-PCR to determine their genetic relatedness. Out of 200 raw milk samples, 46.5% tested positive for non-STEC, 39.5% showed the presence of S. Typhimurium, and 11% were positive for STEC. The two genotyping tools showed different discrimination indexes, with BOX-PCR exhibiting a higher index mean (0.991) compared to ERIC-PCR (0.937). This suggested that BOX-PCR had better discriminatory power for genotyping the bacteria. Our study provides information on the safety of milk sourced from dairy farms, underscoring the importance of regular inspections and surveillance at the farm level to minimize the risk of E. coli and Salmonella outbreaks from milk consumption.