The Japanese anchovy, Engraulis japonicus, is an important economic fish that is distributed in the northwest Pacific Ocean. The effective assessment and management of the Engraulis japonicus fishery requires reliable information regarding its population’s genetic structure. The recent development of double digest restriction-site associated DNA sequencing (ddRAD-Seq) methods may contribute to the discovery of SNPs and the assessment of genetic structure. In our study, 98 single nucleotide polymorphism (SNP) markers were developed using ddRAD-Seq. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.3333 to 0.8000 and 0.2778 to 0.5000, respectively. The polymorphism information content (PIC) ranged from 0.239198 to 0.375. All loci have been substantiated to follow the Hardy–Weinberg equilibrium. These novel polymorphic SNP markers will play an important role in the genetic research of E.japonicus, which will be beneficial to the development and utilization of E.japonicus resources. This study aims to provide technical support for the research of genetic diversity of E. japonicus populations through the development of SNP markers.

日本鳀鱼Engraulis japonicus是分布于西北太平洋的重要经济鱼类。 Engraulis japonicus渔业的有效评估和管理需要有关其种群遗传结构的可靠信息。双酶切限制位点相关 DNA 测序 (ddRAD-Seq) 方法的最新发展可能有助于 SNP 的发现和遗传结构的评估。在我们的研究中，使用 ddRAD-Seq 开发了 98 个单核苷酸多态性 (SNP) 标记。观察到的杂合度 (Ho) 和预期杂合度 (He) 的范围分别为 0.3333 至 0.8000 和 0.2778 至 0.5000。多态性信息含量(PIC)范围为0.239198至0.375。所有基因座均已被证实遵循哈代-温伯格平衡。这些新型多态性SNP标记将在日本刺参遗传研究中发挥重要作用，有利于的开发利用>种群。大肠杆菌遗传多样性研究提供技术支撑。通过开发 SNP 标记来识别日本刺参资源。本研究旨在为刺参