Alligators and caimans split in North America during the early Tertiary or late Cretaceous (about 53 million[2] to about 65 million years ago[1]) and the latter reached South America by the Paleogene, before the closure of the Isthmus of Panama during the Neogene period.

Traditionally, crocodiles and alligators were considered more closely related and grouped together in the clade Brevirostres, to the exclusion of the gharials.

This classification was based on morphological studies primarily focused on analyzing skeletal traits of living and extinct fossil species.

[10] However, recent molecular studies using DNA sequencing have rejected Brevirostres upon finding the crocodiles and gavialids to be more closely related than the alligators.

[11] A 2018 tip dating study by Lee & Yates simultaneously using morphological, molecular (DNA sequencing), and stratigraphic (fossil age) data established the inter-relationships within Crocodilia,[9] which was expanded upon in 2021 by Hekkala et al. using paleogenomics by extracting DNA from the extinct Voay.