The sea raven, Hemitripterus villosus, is a common species in the northwestern Pacific Ocean. Owing to the significant role of the sea raven in the flesh and caviar industries, it has become one of the economically important species in China, Korea, and Russia. Owing to the decrease in resources for sturgeons in the caviar industry, sea raven is one of the best alternative candidates. However, due to anthropogenic activities, such as overfishing and pollution, the fishery resources for sea raven have been overexploited and have declined in recent years. Further, due to limited biological and genetic information on this species in Chinese coastal waters, the development of resource management and conservation, as well as fisheries and related processing industries, have been markedly restricted. To obtain useful genetic information to implement sound management and conservation plan, whole-genome analysis based on high-throughput sequencing data was performed to estimate basic genomic information and develop genome-wide genetic markers of this species at low cost. Genomic information was estimated based on the k-mer distribution pattern (k=17) using GCE v1.0.0 software. The genome sequence was then assembled to contig and scaffold levels using SOAPdenovo v2.01 software, with k=41. Subsequently, genome-wide microsatellite motifs were identified using MISA software. Primers were designed using Primer3 software. A total of 52.04 Gb of clean sequencing data was generated. K-mer analysis revealed that the genome size of H. villosus was approximately 713.18 Mb, with a heterozygosity rate of 0.26% and repeat sequence rate of 38.61%. Based on preliminary genome assembly results, the Contig N50 and Scaffold N50 were 7433 bp and 19 388 bp, respectively, with a final sequence size of approximately 577 Mb and GC content of 43.49%. The levels of continuity and completeness of this assembly were low; hence, further studies are needed for improved high-quality genome assembly. Based on the assembled genome sequence, 583 498 microsatellite motifs were detected throughout the genome, with a relative abundance of 1010 microsatellite motifs per Mb. Among them, the ratio of dinucleotides was the highest (55.61%), followed by that of mononucleotides (33.39%). AC/GT and AGG/CCT were dominant in the dinucleotides and trinucleotide repeats, respectively, and the repeated copy number of microsatellites mainly ranged from 5 to 17 times. To preliminarily validate the effectiveness of identifying microsatellites, ten motifs were randomly selected for primer design. After PCR amplification and electrophoresis detection, nine microsatellite motifs were successfully amplified. However, further confirmation is still needed to validate the effectiveness of identifying microsatellites and their polymorphisms at the population level. The genome survey results revealed a simple genome of H. villosus, which could be assembled using the sequencing strategy of “Illumina+PacBio+Hi-C” to generate a high-quality chromosomal level genome assembly. The screened microsatellite loci could also be used as effective molecular markers for subsequent genetic studies. Owing to the limitations of our study, further analyses are needed to improve the quality of genome assembly, confirm the effectiveness of the identified microsatellite loci in population genetic studies, and conduct comparative analyses between samples from different geographic localities. The findings of this study provide not only basic information for evolutionary biology and genetic assessments of the sea raven, H. villosus, but also scientific references for fishery and germplasm resource management and conservation from a genetic perspective.