Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which plays a key role in the transmission of human blood fluke Schistosoma. The complete mitochondrial (mt) genome of O. hupensis has been characterized; however, the phylogenetic performance of mt protein-coding genes (PCGs) of the snail remain unclear. In this study, 11 whole mt genomes of snails collected from four different ecological settings in China and the Philippines were sequenced. The mt genome sizes ranged from 15 183 to 15 216 bp, with the G + C contents from 32.4% to 33.4%. A total of 15 251 characters were generated from the multiple sequence alignment. Of 2711 (17.8%) polymorphic sites, 56.22% (1524) were parsimony sites. The mt genomes‘ phylogenetic trees were reconstructed using minimum evolution, neighbor joining, maximum likelihood, maximum parsimony, and Bayesian tree estimate methods, and two main distinct clades were identified: (i) the isolate from mountainous regions; (ii) the remaining isolate which included three inner branches. All phylogenetic trees of the 13 PCGs were generated by running 1000 bootstrap replicates and compared with the complete mtDNA tree, the classification accuracy ranging from 21.23% to 87.87%, the topological distance of phylogenetic trees between PCGs ranging from 5 to 14. Therefore, the performance of PCGs can be divided into good condition (COI, ND2, ND5, and ND3), medium (COII, ATP6, ND1, ND6, Cytb, ND4, and COIII), poor (ATP8 and ND4L). This study represents the first analysis of mt genome diversity of the O. hupensis snail and phylogenetic performance of mt PCGs. It presents clear evidence that the snail populations can be separated into four landscape genetic populations in mainland China based on whole mt genomes. The identification of the phylogenetic performance of PCGs provides new insight into the intensive genetic diversity study using mtDNA markers for the snail.