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Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens ( n  = 2) of the extinct “horned” crocodile,  Voay robustus , collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between  Voay  and  Crocodylus  (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed  Voay  within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between  Voay  and  Crocodylus  lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of  Voay  from Madagascar.

Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus