Freshwater mussels have suffered a severe decline during the last century. Accurate description and identification of species have been an arduous and important task for the conservation of this group. Recently, with the promotion of molecular technology, especially mtDNA, many morphological species have been merged. In the genus Lamprotula, L. caveata, L. cornuumlunae and L. leaii are recognized as valid species. The complete mitogenome of. L. cornuumlunae was firstly sequenced in this study. By comparing mitochondrial genomics and phylogenetic analysis, the results showed that mtDNA cannot distinguish between L. caveata and L. cornuumlunae. We hypothesized that the deficiencies of mtDNA in species delimitation was caused by very recent speciation. Time-calibrated multilocus divergence time estimation revealed that L. caveata and L. cornuumlunae recently diverged in the Neogene Pliocene. This study presents the potential problems of relying on mtDNA sequences for delimiting recently diverged species. We emphasis that mtDNA cannot be used solely or dominantly to understand biodiversity. Instead, it is indeed an effective tool, combined with more data, such as shell morphology, reproductive characters and biogeography, to integrate species concepts.