Abstract: The sequence homology and molecular evolution of Hoxa3a gene were analyzed in common carp and other fishes and organisms by some bioinformatics softs.The results showed that the maximal sequence homology（up to 95%） was observed in common carp（Cyprinus carpio） and zebrafish（Danio rerio）,followed by Atlantic salmon（Salmo salar）,Japanese pufferfish（Takifugu rubripes）,Japanese medaka（Oryzias latipes） and Cichlid fish（Astatotilapia burtoni）（about 84%）,and the minimal（74.5%） in other fishes such as lttle skate（Leucoraja erinacea） and Australian ghost shark（Callorhinchus milii）.The sequence homology of common carp with three non-fish organisms was found to be 75%.This result also showed that Hox gene sequences were highly conserved evolutionarily.In the sequence comparison at the same time,two common carp SNP sites 101 site（T/C） and 213 site（C/T） were found.The result has great significance for the conservation of biological diversity（particularly genetic diversity） study and reveals the progress and mechanism of biological evolution.

Key words: common carp, homeobox gene（Hox gene）, sequence homology, molecular evolution, SNP