Analyses of proteins, lipids and nucleic acids have been extremely useful for assessing the level of molecular divergence in the Crocodilia and for inferring the relationships of crocodilians to each other and to other vertebrates. A large body of traditional (morphological and paleontological), as well as recent non-traditional (cytogenetic and molecular) evidence concurs that birds are the closest living sister group to the Crocodilia. Relationships within the order have been much more difficult to resolve using traditional analyses due to the problems of convergence/parallelism and general morphological conservatism. Studies of protein divergence, while in agreement with traditional interpretations of affinities between the alligators and caimans, suggest that the true and false gharials are more closely related to each other than to other crocodilians and that the true crocodiles are all very close relatives that may have diverged recently. Preliminary analyses from an ongoing study of restriction endonuclease analysis of crocodilian mitochondrial and ribosomal DNAs corroborate both of these observations, suggesting that the molecular approach will be very valuable for resolving crocodilian phylogeny.