The Chinese tapertail anchovy,Coilia nasus, is a socioeconomically important anadromous fish that migrates from near ocean waters to freshwater to spawn every spring. The analysis of genomic architecture and information ofC. nasuswere hindered by the previously released versions of reference genomes with gaps. Here, we report the assembly of a chromosome-level gap-free genome ofC. nasusby incorporating high-coverage and accurate long-read sequence data with multiple assembly strategies. All 24 chromosomes were assembled without gaps, representing the highest completeness and assembly quality. We assembled the genome with a size of 851.67 Mb and used BUSCO to estimate the completeness of the assembly as 92.5%. Using a combination ofde novoprediction, protein homology and RNA-seq annotation, 21,900 genes were functionally annotated, representing 99.68% of the total predicted protein-coding genes. The availability of gap-free reference genomes forC. nasuswill provide the opportunity for understanding genome structure and function, and will also lay a solid foundation for further management and conservation of this important species.