First appearing in the latest Cretaceous, Crocodylia is a clade of mostly semi-aquatic, predatory reptiles, defined as all of the descendants of the last common ancestor of the extant alligators, caimans, crocodiles, and gharials. Crocodylian phylogeny has been extensively studied using molecular and morphological datasets; however, numerous systematic problems exist, notably the disagreement between these datasets over the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. I constructed a new morphological dataset for Crocodylia, through (1) an anatomical reappraisal of a ‘basal’ crocodylian taxon, Diplocynodon hantoniensis; (2) a critical reappraisal of published character data matrices; and (3) extensive, first-hand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs and 330 characters) including a new, illustrated character list, modifications to the construction and scoring of most characters, and 45 novel characters. Nine phylogenetic analyses under maximum parsimony compared the effects of weighting strategies and the treatment of quantitative characters. In agreement with the molecular hypothesis, and for the first time based on morphology alone, Gavialis is recovered as more closely related to Tomistoma than to any other extant crocodylian. This result is recovered in all analyses; however, those using continuous characters and extended implied weighting (with a high k-value) produce the most reliable and stratigraphically congruent topologies. Nevertheless, temporal incongruence between morphological and molecular datasets exists, indicating that several putative gavialids require reappraisal. New interrelationships are discussed along with a comprehensive review of their evolutionary and biogeographic implications, including: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) recovery of the early Paleogene South American taxon Eocaiman as a ‘basal’ alligatoroid; and (3) modifications to the taxonomic content of Mekosuchinae, suggesting biogeographic affinities of this Australasian clade with latest Cretaceous–early Paleogene Asian crocodyloids.