Phylogeny of 25 Hemidactylus frenatus populations from Taiwan and adjecent islands were resloved by mitochondrial cytochrome b nucleotide sequences and morphological characters. A total of 327 bp were sequenced. Using neighbor-joining and maximum parsimony methods, the phylogenetic trees divide Hemidactylus frenatus into 8 regional groups: Tungshia group; Chiaohsi group; northwest group; central group; Chiayi-Tainan group; south-Penghu group; east-Hengchun group; and southeast group. The results suggest that, the dispersal center should be in the northwest, and then dispersed to the east and the south. Phylogenetic state of Chiaohsi population is not clear. It may be immigrated from northwest or outside of Taiwan. The Penghu and Kaohsiung populations have a short genetic distance, maybe caused from frequently genetic interflow, as well as the Chihpen, Tunghe, Lutao and Lanyu populations. The Principle Component Analysis and Canonical Discriminate Analysis of 16 morphological characters, showed that no differences exist populations.

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