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The synthesis of a microbial flocculant is strictly controlled by its genetic genes, which may be the result of the expression of flocculant genes in the microbial genome. The whole genome of Klebsiella pneumoniae M1 was sequenced for obtaining the mechanism of flocculant synthesis and exploring the mechanism of flocculant production by flocculant bacteria. Therefore, it provided a basis for molecular genetics and functional genomic analysis of flocculants production bacteria. In this way, the mechanism of flocculant production by flocculating bacteria can be better explored. The whole genome sequence of flocculant strain M1 was determined using advanced second generation (Illumina) and third generation (PacBio) sequencing, which was screened from wheat alcohol wastewater. The genes related to flocculant characteristics produced by strain M1 were analyzed for combining with the analysis of flocculant structure characteristics. According to the de novo assembly, a total of 5,511,794 bp clean reads were generated and assembled into 24 contigs. The GC content was up to 58.39%. The genome contained approximately 5383 genes, but 5348 genes had obvious biological functions. A total of 437 genes were involved in carbohydrate metabolism and had coding genes of five carbohydrate-related enzymes. This result indicated that there were functional genes closely related to polysaccharide production in M1 genome. The main metabolic process of flocculant strain Klebsiella pneumoniae M1 was closely related to the potential pathway of extracellular polysaccharide biosynthesis, in which five kinds of carbohydrate synthase genes were involved.