The objectives of this study are: 1) to determine population genetic differentiation based on the control region of mtDNA data of small rodents, 2) to examine that whether the habitat islands constitute a geographical barriers for gene flow of small mammals in Yusan National Park, finally, 3) to provide the information for public conservation education and park planning. The results of this study show Apodemus semotus was the dominant species in all trapping sites, including the Mts. Guan, Yuan, and Shokulan and Tataka area. The phylogeographic structure in the control region of mt DNA of A. semotus, Niviventer culturatus and Microtus kikuchii were analyzed. The phylogenetic trees are constructed by Neighbor-joining method. There were little phylogeographic patterning among the trapping localities of A. semotus and N. culturatus. However, the phylogenetic analysis of M. kikuchii revealed that the four lineages distinct separated. It may be concluded that the topography of the mountain ranges of Taiwan play the important role as a barrier against gene flow for the highland species. In future, the conservation strategy of Yushan National Park should be considered about the ecology of mountain-island habitats.