Anchovies (Engraulidae) are one of the ecologically important groups and often difficult to identify due to their small size and overlapping morphological characters. In the present study, reference DNA barcodes were generated for 82 individuals representing 13 species of Engraulidae family using mitochondrial Cytochrome c oxidase subunit I (COI) and 16S rRNA genes. The average genetic distance value of COI gene for conspecific, congeneric and confamilial is 0.25, 20.45 and 22.28%, respectively. Mitochondrial 16S rRNA showed an average divergence value of 0.60, 10.28 and 14.37% for within species, between species and within families, respectively. Comparison of the present study reference barcodes with the reported sequences revealed high frequency of misidentification of species and possible occurrence of cryptic species in this family. Phylogenetic tree reconstructed using different methodologies revealed monophyletic nature of genus Stolephorus and the evolutionary relationship within genus Stolephorus is defined as ([S. insularis: S. tamilensis] S. dubiosus (S. waitei [S. commersonnii: S. indicus])).

凤尾鱼（Engraulidae）是重要的生态类群之一，由于其体型小和形态特征重叠而常常难以辨认。在本研究中，使用线粒体细胞色素c氧化酶亚基I（COI）和16S rRNA基因，为代表13种of科的82个个体生成了参考DNA条码。同种，同系和同系的COI基因的平均遗传距离值分别为0.25、20.45和22.28％。线粒体16S rRNA物种内，物种间和科内的平均差异值分别为0.60％，10.28％和14.37％。本研究参考条形码与已报道序列的比较表明，该家族中物种错误识别的频率很高，并且可能出现隐性物种。用不同的方法重建的系统发育树揭示了Stolephorus属的单系性，并且将Stolephorus属内的进化关系定义为（[ S. insularis：S。tamilensis ] S. dubiosus（S. waitei [ S. commersonnii：S。indicus ]）） 。