Savalani hairtailLepturacanthus savalais a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly ofL. savalawas obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembledL. savalagenome was 790.02 Mb with contig N50 and scaffold N50 values of 19.01 Mb and 32.77 Mb, respectively. The assembled sequences were anchored to 24 chromosomes by using Hi-C data. Combined with RNA sequencing data, 23,625 protein-coding genes were predicted, of which 96.0% were successfully annotated. In total, 67 gene family expansions and 93 gene family contractions were detected in theL. savalagenome. Additionally, 1825 positively selected genes were identified. Based on a comparative genomic analysis, we screened a number of candidate genes associated with the specific morphology, behaviour-related immune system, and DNA repair mechanisms inL. savala. Our results preliminarily revealed mechanisms underlying the special morphological and behavioural characteristics ofL. savalafrom a genomic perspective. Furthermore, this study provides valuable reference data for subsequent molecular ecology studies ofL. savalaand whole-genome analyses of other trichiurid fishes.