AbstractWe analyzed DNA sequences of the mitochondrial cytochrome b gene (cyt b), the nuclear Recombination Activating Gene 1 (RAG1) and the myelocytomatosis oncogene (MYC) to infer the phylogenetic relationship of Caiman crocodilus and Caiman yacare, and other South American alligatorid crocodilian species. Phylogenetic relationships were robustly supported with Paleosuchus sister to Melanosuchus and Caiman. Phylogenetic relationships of C. crocodilus and C. yacare were unclear as these two species share mitochondrial and nuclear haplotypes. Specifically this sharing occurs among specimens of C. yacare and C. crocodilus from the Madeira River drainage. Two potential explanations stand out: secondary contact followed by hybridization, and differentiation along a cline. Current data cannot resolve between these two competing hypotheses. In comparison with C. yacare and C. crocodilus, Paleosuchus trigonatus and Paleosuchus palpebrosus are very well differentiated and also show surprising haplotypic diversity in spite of their phenotypic similarity. J. Exp. Zool. 309A:588–599, 2008. © 2007 Wiley‐Liss, Inc.