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Abstract: Phylogenetic trees are an important tool to help in the understanding of relationships between objects that evolve through time, in particular molecular sequences. In this paper, we efficiently solve two subtree-comparison problems on a set of phylogenetic trees which have practical applications to analyze the evolution and co-evolution genes clustering of genomic sequences. Let be a set of k phylogenetic trees such that the leaves of each tree are drawn from and the leaves for two arbitrary trees are not necessary the same, where n is the maximum number of the leaves among the k trees. We present a linear-time algorithm to find all the leaf-agreement descendant subtrees. By further extending this result, we present a linear-time algorithm to find all the leaf-agreement isomorphic descendant subtrees. Based on our algorithms, a web-based system using input tree files from TreeBASE is also implemented. [Copyright &y& Elsevier]