Fossil crocodylian remains have been documented from India and other parts of South Asia since the mid-19th century, but specimens attributed to several extinct and extant species of Crocodylus have largely been neglected in modern taxonomic treatments. Here, we present a detailed anatomical description of the extinct species Crocodylus palaeindicus, which we restrict to the Late Miocene to early Middle Pleistocene of India. Using an autapomorphy-based approach to species-level identification, we regard Crocodylus sivalensis as a junior synonym of C. palaeindicus, and provide taxonomic reidentifications of all specimens previously referred to these two species. We present a new diagnosis for C. palaeindicus that facilitates its distinction from the extant mugger crocodile, C. palustris, which does not unequivocally appear in the fossil record prior to the Pleistocene. The lack of clear spatiotemporal overlap, coupled with the otherwise lengthy ghost lineage implied by their sister taxon relationship in our phylogenetic analyses, provides tentative support that the extant species is either the descendant of C. palaeindicus, or originated via budding cladogenesis. An expanded phylogenetic analysis recovers the Late Miocene African C. checchiai and Pliocene South American C. falconensis as species within the Neotropical Crocodylus clade, supporting an African origin for this radiation. We also recover Kinyang, from the early–middle Miocene of Kenya, as a crocodyline, rather than an osteolaemine as originally described, and it is potentially the stratigraphically earliest known member of the Crocodylus lineage. Other notable results from our phylogenetic analyses suggest that crocodyloids might not have been present in North America prior to the late Neogene arrival of Crocodylus, with Albertosuchus knudsenii, Prodiplocynodon langi, and ‘Crocodylus’ affinis all recovered outside of Crocodyloidea. Furthermore, we demonstrate that an alligatoroid placement for the recently erected latest Cretaceous–Paleogene East Asian clade Orientalosuchina is highly labile, with relationships at the ‘base’ of Crocodylia unstable.

The morphological data matrix was built based on the literature and personal observations. These data were then analysed under the TNT (v. 1.6) software for phylogenetic inferences with several methods of inference.