In order to investigate the contamination status of Sal-monella in fresh pork and fresh chicken, and research its whole genome characteristics and molecular traceability, the laboratory randomly collected 24 fresh pork and 27 fresh chicken from the fresh market in Changsha, were inspected according to “National Food Safety Standard Food microbiological examination: Salmonella” GB 4789.4—2016. The results showed that in 24 randomly selected fresh pork, 20 samples were detected, with the detection rate of 83.3%; in 27 randomly selected fresh chicken, 20 samples were detected, and the detected rate is 74.1%; the total detection rate was 78.4%. The results showed that the fresh pork and fresh chicken sold on the fresh market in Changsha were seriously contaminated by Salmonella, which had great risk for food safety. 40 of them were analyzed by whole genome sequencing and molecular traceability analysis. The results showed that 20 kinds of pig-derived Salmonella strains and 20 kinds of chicken-derived Salmonella strains could be divided into 5 clusters, and clearly reflected the distribution of pollution sources and cross-contamination of Salmonella, achieving precise traceability. 15 pathogenic genes were found, which clarified the possible pathogenic genes and pathogenic mechanisms on the genetic level, and suggested the potential risk of Salmonella. The research on the pathogenic mechanism of related diseases provided guidance for diseases control. 15 genes involved in drug-resistance were found, which clarified the possible drug-resistant genes and the relative mechanisms on the genetic level, providing important data for the control of highly drug-resistant strains.