Constructing the phylogenetic tree of life is an important resort of learning the origin and the evolution among species.By introducing the concept of "kernel"

a method to achieve phylogenetic tree based on KEGG metabolic pathway is presented.We firstly solved the problem of pathway abstraction with no metabolic information lost

and secondly we defined the similarity between different metabolic pathways as the summation of weighted matching score of the kernel subgraph and the non-kernel one respectively.Based on the distance matrix obtained by the two steps above

we construct the phylogenetic tree of several species.The experiments show that it is an efficient method according to the comparison between the trees obtained and NCBI taxonomy.