To elucidate the distribution of microsatellites in the genomes of Sebastes schlegelii and Sebastiscus marmoratus, the MISA software was employed to search for and compare microsatellite sequences across both genomes. The results indicated that the total length of the S. schlegelii genome sequence was 848 024 649 bp, comprising 741 sequences, of which 635 contained 534 272 microsatellite loci. The total length of microsatellite sequence was 14 151 681 bp, with an average of one microsatellite locus per 1 587.25 bp, representing 1.67% of the genome. Of the sequences containing microsatellite loci, 584 (91.97%) contained more than one locus, while 51 (8.03%) contained a single locus. The ratios of different repeat types of microsatellites, ranked by size, were as follows: di-nucleotide (46.37%) > mono-nucleotide (30.97%) > tri-nucleotide (15.42%) > tetra-nucleotide (5.7%) > penta-nucleotide (1.19%) > hexa-nucleotide (0.35%). For S. marmoratus, the total genome sequence length was 795 691 141 bp, with a total of 90 sequences. Among these, 77 sequences contained 571 370 microsatellite loci. The total length of microsatellite sequences was 15 854 826 bp, with an average of one microsatellite locus per 1 392.60 bp, accounting for 1.99% of the genome. Of the sequences containing microsatellite locus, 74 (96.10%) contained more than one locus, while 3 (3.70%) sequences contained a single locus. The ratios of different repeat types of microsatellites, ranked by size, were di-nucleotide (47.63%) > mono-nucleotide (32.90%) > tri-nucleotide (13.63%) > tetra-nucleotide (4.26%) > penta-nucleotide (1.04%) > hexa-nucleotide (0.53%). Our findings demonstrate that the microsatellites of different repeat types in S. schlegelii and S. marmoratus exhibit similar characteristics. Additionally, as the amplification length of microsatellite sequences increased, the frequency of nucleotides in both fish species showed a gradual downward trend. This study, which compared the distribution of microsatellites in the genomes of S. schlegelii and S. marmoratus, provided a foundation for future research on microsatellite marker screening, genetic analysis, and molecular breeding of these two species.