Stenotrophomonas maltophilia is one of the major pathogens causing high lethality and infectious diseases of Ictalurus punctatus in recent years. In order to provide technical reserves for the prevention and treatment of this disease, S. maltophilia XH.SM.1 strain was subjected to whole genome sequencing and comparative genomics analysis, and its morphological characteristics were observed by scanning electron microscopy. Electron microscopic observation showed that the short rod-shaped bacteria at both ends of XH.SM.1 had a length of about (1.73±0.35) μm and a width of about (0.43±0.04) μm. XH.SM.1 strain contained a chromosome of 4.56 Mb with an average G+C content of 66.60%, 4 087 coding sequences (CDS).The genomic sequence was uploaded to NCBI and obtained accession number:PYBO01000001.1. By comparing with the VFDB database, three virulence genes with a higher confidence level were predicted. The results of collinear analysis showed that XH.SM.1 had good collinearity with 10 S. maltophilia at the level of completion. ARDB database prediction and genomic island analysis found that XH.SM.1 contains many drug resistance genes. The results of pan-genomic analysis showed that XH.SM.1 showed an open result, which is consistent with the phenotype of the pathogenic bacteria that are often found in the environment, indicating that it can adapt to the environment and the outside world. Its ability to communicate with genetic material is better.