Abstract: The genome DNA was extracted respectively from Acanthoscelides macrophthalmus and Bruchidius terrenus, and the COX1 and 12S rRNA genes were sequenced and analyzed to establish the basis for the further molecular study. The results showed that COX1 and 12S rRNA of the two beetle species presented higher content of A+T, nucleotide C and T showed higher conversion rate. The two genes had codon usage bias as using codons with the third base A or T. It was showed that Acanthoscelides macrophthalmus shared a longer distance with Bruchidius terrenus, but a shorter distance with Acanthoscelides oblongoguttatus. While, Bruchidius terrenus would be grouped into the same branch of the genus Bruchidius. However, the more accurate phylogenetic roles of Acanthoscelides macrophthalmus and Bruchidius terrenus need to be further studied due to limited nucleotide data in GenBank.