Abstract: In this study, bioinformatics methods were used to analyze and compare the genome-wide characterization of microsatellites in the chromosome-level genomes (2.62 and 2.50 Gb respectively) of the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis; YFP) and the East Asian finless porpoise (N. a. sunameri; EAFP). The results showed that a total of 888424 and 867792 perfect microsatellites were identified in the whole genomes of the YFP and the EAFP, with a total length of 1534077 and 1472448 bp respectively, accounting for about 0.59% of the whole genome sequences. In both the YFP and EAFP genomes, the numbers of the six major repeat types of perfect microsatellites were similar, with mononucleotide repeats being the most abundant, followed by dinucleotide, hexanucleotide, tetranucleotide, trinucleotide, and pentanucleotide repeats. The most abundant repeat motifs in the two genomes were A, AC, AT, CCCTAA, and AGGGTT. Additionally, we also analyzed the microsatellite distribution characteristics in the Y chromosomes of the YFP and EAFP. In total, 6195 and 5024 perfect microsatellites were detected in the Y chromosome respectively. Among the six repeat types of perfect microsatellites on the Y chromosomes, mononucleotide repeat was also the most abundant type, followed by dinucleotide, tetranucleotide, trinucleotide, pentanucleotide, and hexanucleotide. In addition, A, AC, and AAT repeat motif categories were the most dominant. In this study, we examined the distribution characteristics and disparities of microsatellites in the chromosomal-level genomes of the YFP and the EAFP, thereby establishing a solid foundation for future research on the development and utilization of species specific microsatellite markers.