Abstract: 【Objective】The distribution and characteristics of microsatellite sequences were searched and analyzed in the genome of Mastacembelus armatus, which could provide a theoretical basis for the evaluation of M. armatus germplasm resources and marker-assisted breeding. 【Method】Based on genomic sequence data of M. armatus, microsatellite loci were searched by MISA software and their distribution and composition characteristics in the genome of M. armatus were evaluated by bioinformatics analysis. 【Result】19020 microsatellites were obtained from genome of M. armatus including 16025 perfect microsatellites. The number of microsatellites distributed on chromosome 2 was the most, and the least was on chromosome 24, which accounting for 10.26% and 1.94% of the total number of microsatellites respectively.Mononucletide was the most abundant microsatellite while hexanucleotide was the lowest. The first four types of perfect microsatellites in the genome of M. armatus were A/T, AC/GT, G/C and AG/CT, which accounting for 37.82%, 29.57%, 6.88% and 6.77% of the total number respectively. The range of the repeat times of motifs was 5-104 with the main repeat times including 5-6 and 10-11. The length interval of microsatellites was 10-192 bp, and the main length interval was 10-36 bp, which taking up 92.46% of the total number. The maximum number of microsatellites was 12 bp in length, which accounting for 15.22% of the total number of microsatellites. Pearson correlation analysis showed that there was extremely significantly negative correlation between the length and number of microsatellites for M. armatus(P<0.01). Functional annotation and analysis of GO showed that microsatellites genes were mainly enriched in three groups including biological process, molecular function and cellular component, and nucleus was the most significantly enriched term. 【Conclusion】The microsatellites obtained based on the genome of M. armatus have high availability and polymorphism potential, which can provide genetic data for the efficient development of microsatellite molecular markers.