In this study, the microsatellite search software MISA was used to search for the perfect microsatellite in the whole genome of three Culterinae species, and its distribution pattern was analyzed. As a result, in the genome of （Culter alburnus,1.055 Gb）, （Anabarilius grahami,1.006 Gb）, and （Megalobrama amblycephala,1.116 Gb）, 772 276, 548 726, and 772 329 perfect microsatellites were screened out, respectively. The relative frequency were 732.0/Mb, 553.2/Mb, and 691.2/Mb, respectively. The total lengths of the microsatellites were 14.29 Mb, 9.42 Mb, and 15.02 Mb, respectively, accounting for 1.35%, 0.94%, and 1.35% of the total length of the genome sequence. Among the complete microsatellites with 1-6 different base repeat types, the orders of 6 base types from the three species of Culterinae were the same. Each had the largest number of mononucleotide repeats, followed by dinucleotide repeats, tetranucleotide repeats, trinucleotide repeats, pentanucleotide repeats, and hexanucleotide repeats. The highest frequency core repeat categories of trinucleotide and tetranucleotide in the three species of fish is AAT and AGAT, respectively. However, the number of AT is more than AC repeat in the dinucleotide of Culter alburnus. The distribution frequency of microsatellites of different base types in the three fish species decreased with the increase of the copy number and length of the repeat units. The length of the microsatellites repeat unit was mainly 10-30 bp, accounting for 90.54%, 94.27%, and 89.17% of the microsatellites, respectively. The results of this study may provide a reference for the further study of Culterinae genome characteristics and contribute basic data for future investigations into molecular marker-assisted breeding and genetic information assessment of 3 Culterinae species.