Freshwater bivalves from the family Unionidae usually have two very divergent mi-togenomes, inherited according to the doubly uniparental model. The early divergenceof these two mitogenomic lineages gives a unique opportunity to use two mitogenomicdata sets in a single phylogenetic context. However, the number of complete sequencesof the maternally inherited mitogenomes of these animals available in GenBank greatlyexceeds that of the paternally inherited mitogenomes. This is a problem for phylogeneticreconstruction because it limits the use of both mitogenomic data sets. Moreover, sincelong branch attraction phenomenon can bias reconstructions if only a few but highlydivergent taxa are considered, the shortage of the faster evolving paternally inheritedmitogenome sequences is a real problem. Here we provide, for the first time, completesequences of the M mitogenomes sampled from Polish populations of two species:nativeUnio pictorumand invasiveSinanodonta woodiana. It increases the available setof mitogenomic pairs to 18 species per family, and allows unambiguous reconstructionof phylogenetic relationships among them. The reconstructions based on M and Fmitogenomes which were separated for many millions of years, and subject to differingevolutionary dynamics, are fully congruent.