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.