To investigate the prevalence of integrons and antimicrobial resistance genes in Salmonella recovered from animals in Japan. Forty-eight out of ninety-four (51.1%) Salmonella isolates showed multidrug resistance phenotypes and harboured at least one antimicrobial resistance gene. Twenty-two out of forty-seven (46.8%) Salmonella enterica serovar Typhimurium that were multidrug-resistant were of definitive phage type DT104. Class 1 integrons were identified in 34/94 isolates (36.2%): 21 isolates containing two gene cassettes, aadA2 and bla(PSE-1), and 13 containing one gene cassette, aadA1, aadA2 or bla(PSE-1). Class 2 integrons containing estX-sat2-aadA1 gene cassettes were only identified in Salmonella Enteritidis. The beta-lactamase-encoding gene, bla(TEM), was only detected in S. Typhimurium. The plasmid-mediated quinolone resistance gene, qnrS1, was identified in S. Typhimurium and Salmonella Thompson. Our results characterized integrons and antimicrobial resistance genes in Salmonella of animal origin. To the best of our knowledge, this is the first report of qnrS in Salmonella from Japan and also the first report of qnrS in S. Thompson. Little is known about the molecular basis of antimicrobial resistance in Salmonella isolated from animals. This study provides useful data on the incidence of integrons and resistance genes in Salmonella of animal origin.