The complement system plays an important role in the innate immune response in higher vertebrates. It is involved in cell lysis and initiation of phagocytosis by opsonisation of pathogens and induction engages the cells of the immune system to trigger processes leading to inflammation. The complement system consists of about thirty proteins grouped in five major gene families. These encode for distinct plasma proteins that react with each other forming three activation cascades (alternative, lectin and classical) which converge in a single terminal pathway. This system appears to be highly conserved in vertebrates. However there is a gap in the knowledge in regards to evolution and diversity of the complement system in crocodilians. To address this, we investigated a large number of complement system genes in the recent available genomes of three crocodilian species (Alligator mississippiensis, Crocodylus porosus, and Gavialis gangeticus) and identified 28 genes. These genes were then compared to other vertebrates including reptiles, birds and mammals to further understand the extent of conservation and differentiation of the complement system among the three extant crocodilian families. We surveyed 25 exons, representing seven genes, across 20 species of Alligatoridae and Crocodylidae. Phylogenetic analyses showed that crocodilian complement genes form orthologous clades across species suggesting that they have evolved independently from each other after speciation. As expected, a considerable level of sequence conservation among species was observed. However, we also found a relatively high frequency of DNA substitution in particular among species of Alligatoridae. No correlation between genetic diversity or allele distribution and species’ habitat or geographic distribution was identified. These findings advance our knowledge of the evolution of this innate immune system and the immunogenetic resources generated here are now being used for population genetic and disease association studies.