Abstract: Resolving the genome-wide information of Engraulis japonicus is of great significance to improve the genomics of anchovy fishes. E. japonicus is a small baitfish with important ecological value, widely distributed in the Northwest Pacific Ocean. However, few studies on the genomics of E. japonicus have been reported, and the development of molecular markers is relatively limited, which limits the in-depth study of the genetic evolution of E. japonicus to a certain extent. In this study, we used high-throughput sequencing to characterize the genome of E. japonicus in order to assess the genomic features of the species and to provide genetic information for the development of molecular markers. The characterization results showed that the genome size was about 1430.36 Mb, and its heterozygosity and proportion of repetitive sequences were 1.55% and 53.87%, respectively. The mitochondrial genome length was 1 704 897 467 bp, and the Contig N50 and Scaffold N50 were 493 bp and 599 bp, respectively. Bioinformatics analyses showed that a total of 3 197 721 microsatellite loci were detected throughout the genome, and the relative abundance was as high as 1 875.61 loci/Mb. Among them, the number of two base repeats (75.26%) had a significant advantage over that of the other two, followed by single-base repeats (10.14%). The two-base and three-base repeats were dominated by AC/GT and AGG/CCT, respectively, and the microsatellite repeat copy numbers of 6 and 7 times were the largest, accounting for 19.49% and 12.35%, respectively. Results show that the E. japonicus genome is relatively small but high proportion of repetitive sequences. At the same time, it has a high degree of heterozygosity, which is consistent with the characteristics of the complex genome. This feature may greatly affect its genome assembly effect. The follow-up should be combined with PacBio and Nanopore sequencing technology to assemble a high-quality genome of the E. japonicus. This result can provide a scientific basis for the development of high-quality genome assembly strategy of E. japonicus, and the microsatellite loci screened can provide basic information for the molecular genetics and variation analysis of the species.