Abstract: Based on computing hydrophobic similarities between cytochrome molecules,this paper constructed the phylogenetic trees of cytochrome molecules and discussed their evolutionary relationship.The results indicated that the phylogenetic trees from protein molecular hydrophobic similarity and nonlinear three-dimensional structure can not only agree with those from other methods,but also can overcome the limitations of some methods at a degree,and get better results.The authors suggest that the method presented in this paper may be more effective to study the relationship between those distance proteins in evolution.