Abstract: The whitespotted conger (Conger myriaster) is an important commercial fishery species widely distributed in China’s coastal waters and possesses high economic and nutritional value. However, the lack of reference genome information has hindered in-depth exploration and utilization of its genetic resources. This study conducted a genomic survey of C. myriaster using high-throughput sequencing technology. A preliminary genome assembly yielded a total length of 1 122 560 887 bp, with K-mer analysis estimating the genome size at approximately 989 Mb. The heterozygosity rate and the proportion of repetitive sequences were calculated to be 0.89% and 39.51%, respectively. A total of 630 516 microsatellite loci were identified in the genome, with repeat numbers predominantly ranging from 5 to 10. The occurrence frequency, appearance frequency, and relative abundance of microsatellites were 12.56%, 18.91%, and 561.46 loci/Mb, respectively. Among six categories of perfect microsatellites, dinucleotide repeats accounted for the highest proportion (325 226 loci, 51.58%) and exhibited the greatest relative abundance (289.20 loci/Mb). Analysis of 343 microsatellite motifs revealed that hexanucleotide repeats were the most diverse (201 types), followed by pentanucleotide (94 types), tetranucleotide (32 types), trinucleotide (10 types), dinucleotide (4 types), and mononucleotide repeats (2 types). Different dominant motifs were identified as: A/T (144 508 loci, 71.65%) for mononucleotide, AC/GT (230 768 loci, 70.96%) for dinucleotide, AAT/ATT (17 099 loci, 37.04%) for trinucleotide, ATCC/ATCG (6 233 loci, 16.38%) for tetranucleotide, AATGT/ACATT (7 039 loci, 59.94%) for pentanucleotide, and AACCCT/AGGTTG (1 202 loci, 15.71%) for hexanucleotide. This genomic survey revealed high heterozygosity (0.89%) and repetitive-sequence content (39.51%) in the C. myriaster genome. The comprehensive characterization of microsatellite distribution patterns will provide foundational data for conducting genetic studies on this species.