[Background] Salmonella is an important food-borne zoonotic pathogen that causes a variety of food-borne diseases among humans and animals. [Objective] This research was to investigate the prevalence, antimicrobial resistance and virulence gene of salmonellosis in ducks in Yunnan province. [Methods] A total of 169 liver samples of dead ducks from various regions in Yunnan province were collected for Salmonella isolation, and the isolated strains were subjected to serotyping, drug sensitivity test, and screening for related drug resistance genes and virulence genes. [Results] Forty-eight Salmonella strains were isolated, with the isolation rate being 28.40%. Three serotypes were discovered, of which Salmonella enteritidis was the dominant one. The isolates had a 100% resistance to penicillin G, lincomycin, clindamycin and rifampicin. Each was resistant to at least 6 kinds of 3 categories of antibiotics, and there was one strain resisting as more as 14 kinds, resulting in 22 drug resistance spectra. A total of 5 resistance genes were detected, of which the detection rates of blaTEM and tetB were 27.08% and 22.92%, respectively, while those of tetA, sul2 and EBC were low. Ten virulence genes were detected, and the detection rates of SPI-1 (avrA), SPI-3 (mgtC), SPI-4 (siiD), SPI-5 (sopB) and bcfC were all 100%, whereas those of SPI-2 ssaQ, spvB, spvC, pefA and stn reached above 60%, with cdtB undetected. [Conclusion] S. enteritidis was the dominant serotype in ducks in Yunnan province, with severe drug resistance and multi-drug resistance, and the mechanism of drug resistance was complex. The coincidence rate of resistance gene and phenotype was low, while the detection rate of virulence gene was high. These results provide a reference for the prevention, control and eradication of salmonellosis in ducks in Yunnan province.