Abstract: Previous studies have shown that Bacillus paralicheniformis FA6 strain (FA6), isolated from the intestine of grass carp, has a role in the degradation of various carbohydrates (e.g. amylase or cellulase activity). In order to study the putative mechanisms of action and explore its potential as a probiotic, we used the third-generation sequencing technology to determine its whole genome sequence. Genome assembly, gene prediction and functional annotation were performed by using bioinformatics methods. Besides, we conducted structural and functional comparative genomic analyses between B. paralicheniformis FA6 and four other available Bacillus spp. genomes (two B. paralicheniformis and two B. licheniformis). Sequence analysis showed that the genome of B. paralicheniformis FA6 consists of a single chromosome, with the size of 4450579 bp, and the GC content of 45.9%. The B. paralicheniformis FA6 genome contains multiple food digestion-related genes, including 128 protease genes, 32 lipase genes and 72 glycoside hydrolase genes. In addition, the bacterial genome contains seven genes encoding for lantibiotics. Structural comparative analysis revealed that all five Bacillus spp. genomes share a collinear structural relationship, but genomic features of B. paralicheniformis FA6 are most similar to the two conspecifics. A comparison of metabolic pathways (KEGG) among the five Bacillus spp. strains showed that B. paralicheniformis FA6 has the largest number of genes involved in metabolic and environmental information processing. The numbers of genes in the B. paralicheniformis FA6 genome encoding cellulases, hemicellulases and amylases were 5, 7 and 5 respectively. This is higher than in other four strains, which indicates that B. paralicheniformis FA6 is better adapted for the digestion of plant cell wall polysaccharides. The results of this study indicate that B. paralicheniformis FA6 is highly adapted for the utilization of a broad range of plant metabolites, which may be a reflection of its adaptive evolution in the intestinal tract of grass carp. Moreover, the results of this study will provide a theoretical basis for the application of B. paralicheniformis FA6 as a dietary supplement to aquaculture feed.