The unionid family Margaritiferidae, comprising 12 extant species, is widely distributed across the northern hemisphere in North America, Europe and Asia (Bolotov et al., 2016). Most species in this family have dramatically declined over the last century, with nine of the 12 species assessed as threatened in the most recent IUCN Red List (IUCN, 2016). Among these is the Moroccan pearl mussel Margaritifera marocana (Pallary, 1918), considered one of the 100 most threatened species on the planet (Baillie & Butcher, 2012). This species is now restricted to two small streams in the Oum Er Rbia and Sebou basins and conservation measures are urgently needed (Sousa et al., 2016). Beyond the conservation concern, Unionida are also biologically interesting. They present an unusual mechanism of mitochondrial inheritance called doubly uniparental inheritance (DUI), in which all individuals have the typical maternally transmitted mtDNA (F-type), but the males possess in their germ cells a paternally inherited mtDNA instead (M-type) (Zouros et al., 1994; Breton et al., 2009). So far, DUI has been observed in over 100 species from four bivalve orders (Gusman, Azuelos & Breton, 2017), including three families within Unionida, i.e. Unionidae, Hyriidae and Margaritiferidae (Walker et al., 2006). However, to date, no whole M-type mitogenome has been published for any species belonging to the last two of these families.