Apple snails of the genus Pomacea (Mollusca: Caenogastropoda: Ampullariidae) are native to the Neotropics and exhibit high species diversity. They hold cultural and ecological significance, serving as an important protein source in Peru. However, this genus has also received broad interest worldwide due to its invasive capacity, especially in Southeast Asia, where some species such as Pomacea canaliculata (Lamarck, 1822) and P. maculata Perry, 1810 are considered significant pests. Consequently, most genetic studies have focused almost exclusively on these invasive species. In contrast, few efforts have been made to understand the evolutionary relationships of the South American native species, especially at the genomic level. In this study, we assembled and annotated the mitochondrial genome of two Pomacea species native to the Peruvian Amazon: Pomacea reevei Ampuero & Ramírez, 2023 and P. aulanieri (Deville & Huppé, 1850). Through a comprehensive comparison with available mitogenomes on NCBI, we found that the length and organization of these mitogenomes fall within the range of what is currently known in Pomacea. Comparisons between these mitogenomes with those previously published revealed differences in the overlapping of adjacent genes, the size of certain protein-coding genes (PCGs) and the secondary structure of some tRNAs which are consistent with the phylogenetic relationships between these species. These findings provide valuable insights into the systematics and genomics of the genus Pomacea.