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Using a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female mitogenome (i.e., gene orders MF1 and UF1). Our results suggest that this macroevolutionary jump was completed within a relatively short time interval (95% HPD 201–226 Ma) that coincided with the Triassic–Jurassic mass extinction. Both gene orders have persisted within these clades for ~200 Ma. The monophyly of the so-called "problematic" Gonideinae taxa was supported by all the inferred phylogenies in this study using, for the first time, the M- and F-type mitogenomes either singly or combined. Within Gonideinae, two additional splits in the gene order (UF1 to UF2, UF2 to UF3) occurred in the Mesozoic and have persisted for ~150 and ~100 Ma, respectively. Finally, the mitogenomic results suggest ancient connections between freshwater basins of East Asia and Europe near the Cretaceous–Paleogene boundary, probably via a continuous paleo-river system or along the Tethys coastal line, which are well supported by at least three independent but almost synchronous divergence events. ; The authors wish to thank the Editor and the three anonymous reviewers for helpful remarks and suggestions that improved the quality of the manuscript. This research was developed under ConBiomics: the missing approach for the Conservation of freshwater Bivalves Project N° NORTE-01-0145-FEDER-030286, cofinanced by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by FCT through national funds (UID/Multi/04423/2019). FCT also supported MLL (SFRH/BD/115728/2016). The Russian Ministry of Education and Science (project no. 6.2343.2017/4.6), the Federal Agency for Scientific Organizations (project no. 0409-2015-0143), the Presidium of the Russian Academy of Sciences (scientific program no. 52), and the Russian Foundation for Basic Research, RFBR (project no. 17-45-290066) supported INB. Permits for fieldwork and sampling in Malaysia were issued by the Malaysian Ministry of Higher Education (FRGS/1/2015/WAB13/UNIM//1). ; info:eu-repo/semantics/publishedVersion