To systematically reveal the genome-wide distribution characteristics of microsatellites and the potential functions of microsatellite-related genes in the tufted duck ( Aythya fuligula ), this study based on the published chromosome-level genomic data, employed bioinformatics methods to systematically analyze the genome-wide distribution characteristics of microsatellites and performed functional annotation of genes containing microsatellites located in exonic regions. The results showed that, from the approximately 1,093 Mbp genome sequence of the tufted duck, a total of 585,346 microsatellites with motif lengths of 1-6 bp were identified, with a total length of 13,232,974 bp, accounting for 1.17% of the genome. Among the six repeat types, mononucleotide repeats were the most abundant (68.45%), followed by tetranucleotide (13.97%) and dinucleotide (10.48%) repeats, while pentanucleotide and hexanucleotide repeats constituted the smallest proportions. The base composition of microsatellites showed a clear A-base bias: among mononucleotide repeats, the A copy type was the most frequent; among dinucleotide repeats, the AT copy type was the most abundant; and tetranucleotide repeats were predominantly of the AAAX type. The top ten motifs in tufted duck genome were A, AAAC, AAAT, AT, AAT, C, AC, AAC, AAAAC and AAAAT in a descending order each with more than 9,200 copies, totaling 518,077 copies and accounting for 88.5% of all microsatellites. Chromosome-level distribution analysis revealed a highly significant positive correlation between microsatellite number and chromosome length ( r = 0.993, P <0.001). The Z chromosome exhibited significantly higher relative abundance and density than autosomes, whereas the W chromosome showed substantially lower relative abundance and density. GO annotation results indicated that genes involved in biological processes were the most common. KEGG pathway enrichment analysis identified 135 pathways, with the FoxO signaling pathway, Notch signaling pathway and sphingolipid metabolism being significantly enriched ( P <0.05). The enrichment of these pathways may be associated with migratory adaptation and neural navigation ability in the tufted duck. This study provides the first systematic characterization of genome-wide microsatellite distribution and functional enrichment of microsatellite-associated exonic genes in the tufted duck, laying a foundation for future development of microsatellite markers, population genetic diversity analyses, and investigations into environmental adaptation mechanisms.