Complement genes, a component of the innate immune response, consists of five major gene families which encode for distinct plasma proteins. These are involved in cell lysis and initiation of phagocytosis by opsonisation of pathogens and induction of the immune system to trigger processes leading to inflammation. Crocodilians are considered to be a good model to investigate the evolution and diversity of the immune system. One of the reasons is that these taxa appear to have an effective innate immune system allowing them to cope with a variety of pathogenic challenges due to common injuries sustained during aggressive displays as well as pathogen pressures in certain environments such as stagnant waterholes but usually they do not show signs of infection. Complement genes appear to be relatively conserved among higher vertebrates while that of fish and other poikilothermic vertebrates, which include crocodilians, have been suggested to be more diverse. However, there is limited knowledge of this system in crocodilians as a basis for definitive conclusions. To address this, we analysed and compared the Complement genes from genome sequence resources of three species of crocodilians (Australian saltwater crocodile, American alligator and Indian gharial). Overall, we re-annotated 13 genes and found a high degree of gene conservation when compared with other higher vertebrates. In addition, an unexpected level of polymorphism including non-synonymous substitutions was found among species. To further investigate these polymorphisms, some Complement genes are being surveyed in 20 species of crocodilians. This study will give some understanding as to whether such diversity may have expanded the innate capacity for immune recognition and response in crocodilians.