Abstract: 【Objective】The genes related to Stenotrophomonas maltophilia CA1 colonization and growth promoting characteristics were excavated to lay a foundation for exploring its growth promoting mechanism. 【Method】Nanopole sequencing technology platform was used for whole genome of CA1 sequencing. Compared the genome sequence with GO, NR,KEGG, COG and other databases to obtain gene function annotation information, the function specific genes were analyzed. Meanwhile,sugarcane root exudates were collected by substrate culture,and the effects of the root exudates on the expression of genes related to colonization, chemotaxis and biofilm formation of CA1 were analyzed. 【Result】The genome size of S. maltophilia CA1 was 4371327 bp, carrying 6 plasmids with a GC content of 64.58%, of which 4696genes were predicted by annotation, including 4525 protein coding genes, 87 tRNA, 13 rRNA, and 1 tmRNA. The GO, COG, KEGG, and NR databases successfully annotated 2795, 2078, 2494 and 2584 genes respectively. The genome of the strain presented some functional genes that were associated with plant growth promoting and colonization, such as bacterial chemotaxis(cheA, cheV, cheY), biofilm formation(flhA, flk, flgG), bacterial adhesion(pgaA, mrkD), siderophores(fes, fepA, fecA), ammonia synthesis(gltP, gltB, gltD) and phosphate metabolism(phoR, phoB, pstA).The results of chemotaxis test showed that compared with the control group, the number of colonies under root exudates treatment was significantly increased(P<0.05,the same below), and the relative expression levels of cheA, cheV and cheY genes were increased, and the formation of CA1 biofilm was also significantly increased. 【Conclusion】The root exudates of sugarcane contributed to the chemotaxis and biofilm formation of strain CA1, and increased the expression of chemotaxis related genes. CA1 contains multiple genes related to growth promotion and colonization, which is the molecular basis of its growth promotion characteristics. The bacterial chemotaxis and biofilm formation are the key steps for its colonization and root exudates were conducive to the strain colonization.