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Simple Summary: We constructed a high-quality genome assembly of Eupleurogrammus muticus at the chromosomal level using PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. By combining genomic annotation, comparative genomic analyses, and species attribute information, we identified many candidate genes related to the whip-like tail, innate immunity, and DNA repair of E. muticus, and determined the evolutionary relationship and divergence time between E. muticus and related species. These findings provide important genomic resources for exploring the genetic mechanisms underlying the unique characteristics of E. muticus and fishery resource conservation. Smallhead hairtail (Eupleurogrammus muticus) is an important marine economic fish distributed along the northern Indian Ocean and the northwest Pacific coast; however, little is known about the mechanism of its genetic evolution. This study generated the first genome assembly of E. muticus at the chromosomal level using a combination of PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. The final assembled genome size was 709.27 Mb, with a contig N50 of 25.07 Mb, GC content of 40.81%, heterozygosity rate of 1.18%, and repetitive sequence rate of 35.43%. E. muticus genome contained 21,949 protein-coding genes (97.92% of the genes were functionally annotated) and 24 chromosomes. There were 143 expansion gene families, 708 contraction gene families, and 4888 positively selected genes in the genome. Based on the comparative genomic analyses, we screened several candidate genes and pathways related to whip-like tail formation, innate immunity, and DNA repair in E. muticus. These findings preliminarily reveal some molecular evolutionary mechanisms of E. muticus at the genomic level and provide important reference genomic data for the genetic studies of other trichiurids. [ABSTRACT FROM AUTHOR]