The Scombridae, including bonitos, mackerels, spanish mackerels, and tunas, contains 15 genera and 50 species in the world which has highly economic importance. Among them, 10 genera and 22 species occur in the waters of Taiwan. Conventional systematic studies of Scombridae is based on morphology and osteology. The present study used complete mitochondrial CO I gene ( 1551 bp ) infer the phylogenetic relationships of common Scombridae in Taiwan. A total of 16 species and 3 outgroups sequences were clustered using Neighbor-joining and Maximum parsimony methods. The results of analyses are summarized as (1) Thunnini, Scomberomorini, and Scombrini are all monophyletic. (2) Sardini is not monophyletic and the absence of Synapomorphy among them so that taxa “Sardini” need rediscuss. Because the larvae of Auxis identification is difficult depending on morphological characters, the present study is based on mitochondrial CO I sequencing to distinguish A. rochei and A. thazard. Behinding the eyes of A. thazard exist a melanophore as a result, and it is a lack at A. rochei. Moreover, we using polymerase chain reaction – restriction fragment length polymorphism ( PCR-RFLP ) technology with two restriction enzymes contains BglII and Bpu10I to identify A. rochei and A. thazard. (1) The restriction enzyme BglII cleaved the 1946 bp fragment to 1676 bp and 270 bp in the larvae of A. thazard, and there was no any cutting sites in A. rochei. (2) The restriction enzyme Bpu10I could cleave the 1946 bp fragment to 1183 bp, 551 bp, and 212 bp in the larvae of A. rochei, but there was no cutting sites in A. thazard.