Abstract:By reconstruction of a phylogenetic tree, the phylogeny of IPP isomerase was studied. The results showed that different source IPP isomerase genes form monophyletic clade with 100% bootstrap support, and each clade had different evolution model. 9.8% amino acid sites of IPP isomerase derived from green algal endured positive selection by method of maximum likelihood rate, and the evolutionary pattern of IPP isomerase gene derived from green algal was different from those in higher plants and bacterium.