Objective Identification and drug resistance of two stains of Yersinia aleksiciae (Ya) isolated from different foods were studied, which provided technical reserves for the isolation of the new Yersinia spp. Methods A total of 300 food samples were collected from August 2018 to March 2019, including pork, beef and chicken. Separation culture, biochemical identification, drug resistance test, and whole genome sequencing analysis were performed on the isolated suspected Ya. Results The positive rate of Ya in food samples was 0.7% (2/300). In biochemical identification, Ya was distinguished from Yersinia enterocolitica (Ye) by lysine decarboxylase test, and Ya was positive for lysine decarboxylase while Ye was negative. Ya didn't exhibit natural resistance to ampicillin, cephalosporin I, ticarcillin and other drugs similar to Ye, and the drug resistance was different between the two strains. 16S rRNA, gyrB, rpoD genes were compared by whole genome sequencing to confirm that the two isolates were Ya. Conclusion The two strains of Ya were isolated and found in China for the first time. There was also no report on the isolation of these strains from food. The method provided in this study could be used for the isolation and identification of new Yersinia spp.