Lactobacillus fermentum 9-4 is a purine-degrading probiotic firstly isolated from traditional fermented rice-flour noodles with special characteristics of southern China’s Guangxi Zhuang Autonomous Region. L. fermentum 9-4 could efficiently reduce the purine contents in foods with excellent purine-nucleoside assimilation and purine-metabolizing enzymatic activities. Crude cell lysate of L. fermentum 9-4 showed strong purine degradation abilities on nucleosides including inosine, guanosine, and purines including xanthine and uric acid, indicating a complete purine metabolic pathway to degrade purine substances to allantoin. In this study, the whole genome of L. fermentum 9-4 was sequenced. Its genome consisted of a 2 085 632 bp circular chromosome without plasmid. The GC content of circular chromosome was 51.25%, including 2 089 coding sequences (CDs), 15 rRNA operons and 59 tRNA coding genes. Genetic analysis showed that at least 5 protein coding genes were related to purine lowering ability. In addition, neither toxic virulence factor nor drug resistance gene was identified by searching the virulence factor database and drug resistance gene database, suggesting good safety of L. fermentum 9-4. The results showed that L. fermentum 9-4 has a good potential for the development and utilization as a purine-degrading probiotic for low-purine foods.