© 2016 Asian Pacific Tropical Medicine Press. Objective: To investigate the relationship between antimicrobial resistance characteristics and corresponding genes, and to diversify repetitive element sequence-based PCR (rep-PCR) fingerprinting of three Salmonella serotypes: Rissen, Panama and Stanley, which were isolated from pig farms and slaughterhouses in Chiang Mai and Lumphun Provinces, Thailand. Methods: A total of 90 Salmonella strains were identified using the Kauffman-White scheme. The Kirby-Bauer disk diffusion method was used to investigate resistance phenotypes of 10 antimicrobial agents. Conventional PCR was used to detect 10 antimicrobial resistance genes, additionally, rep-PCR typing method was applied to identify clonality among Salmonella isolates. Results: The antimicrobial susceptibility testing found resistance to ampicillin (80.0%), streptomycin (65.6%), tetracycline (61.1%), sulfamethoxazole (53.3%), chloramphenicol (28.9%), nalidixic acid (6.7%) and cefotaxime (2.2%). All strains were sensitive to amoxicillin-clavulanic acid, ciprofloxacin and norfloxacin. The most common antimicrobial resistance patterns among the isolates were ampicillin, chloramphenicol, streptomycin, tetracycline, and sulfamethoxazole. The type and frequency of antimicrobial genes detected included bla TEM (100.0%), aadA2 (52.2%), cmlA (45.6%), strA (38.9%), tetA(B) (16.7%), sul1 (15.6%), bla OXA-2 (14.4%), bla PSE1 (6.7%), aphA1-lab (2.2%) and blaCMY-2 (1.1%). Conclusions: Statistical analysis revealed no association between antimicrobial resistance genes and resistance profiles with the exception of cmlA and chloramphenicol, sul1 and sulfamethoxazole, aadA2 and streptomycin, and strA and streptomycin (P < 0.05). Finally, the identical groups of clonal strains were detected by rep-PCR indicating similarity among Salmonella genotypes from farms and from slaughterhouses.