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The apple snails <i>Pomacea canaliculata</i>, <i>Pomacea diffusa</i> and <i>Pomacea maculate</i> (Gastropoda: Caenogastropoda: Ampullariidae) are invasive pests causing massive economic losses and ecological damage. We sequenced and characterized the complete mitochondrial genomes of these snails to conduct phylogenetic analyses based on comparisons with the mitochondrial protein coding sequences of 47 Caenogastropoda species. The gene arrangements, distribution and content were canonically identical and consistent with typical Mollusca except for the <i>tRNA-Gln</i> absent in <i>P. diffusa</i>. An identifiable control region (<span style="font-variant: small-caps;">d</span>-loop) was absent. Bayesian phylogenetic analysis indicated that all the Ampullariidae species clustered on the same branch. The genus <i>Pomacea</i> clustered together and then with the genus <i>Marisa</i>. The orders Architaenioglossa and Sorbeoconcha clustered together and then with the order Hypsogastropoda. Furthermore, the intergenic and interspecific taxonomic positions were defined. Unexpectedly, <i>Ceraesignum maximum</i>, <i>Dendropoma gregarium</i>, <i>Eualetes tulipa</i> and <i>Thylacodes squamigerus</i>, traditionally classified in order Hypsogastropoda, were isolated from the order Hypsogastropoda in the most external branch of the Bayesian inference tree. The divergence times of the Caenogastropoda indicated that their evolutionary process covered four geological epochs that included the Quaternary, Neogene, Paleogene and Cretaceous periods. This study will facilitate further investigation of species identification to aid in the implementation of effective management and control strategies of these invasive species.