Gekkonidae (Reptilia: Lepidosauria: Squamata: Sauria: Gekkota) is one of the most primitive group of reptiles. The Gekkonids are widely distributed in the mainland and islands between 49°(N) and 46°(S) and well adapted to a variety of habitats. In this work, 96 individuals of twenty species of Gekkonidae in China and surrounding area were analysed by partial sequences of mitochondrial and nuclear genes fragments of . Molecular phylogenetic trees were reconstructed using maximum likelihood and Bayesian inference methods in MrBayes 3.1.2 and Phyml v3.0 respectively, with Delma tincta and Pygopus nigriceps in Pygopodidae as outgroups. We discussed the molecular phylogeny of the subfamilies and genera in Gekkonidae based on the 12SrRNA and oocite maturation factor Mos gene (c-mos). We deliberated the phylogeny of Gekko and Cyrtopodion. With support from molecular phylogenetic dataand morphological charecteristics, we arranged the taxonomy of some species within Gekko, Hemidactylus and Cyrtopodion(Gekkonidae) and described a new genus named Gigagekko. The phylogenetic tree resulted as follows: (1) The Diplodactylinae was the base of the phylogenetic tree; Gekkonidae and Eublepharidae were sister group. The species of Goniurosaurus, Coleonyx and Eublepharis (Eublepharidae: Eublepharinae) clustered with Aeluroscalabotes felinus (Gekkonidae: Aeluroscalabotinae) and formed a monophyletic group. (2) The Chinese genus Cyrtopodion is not monophyletic with the three species bent-bowed geckos from Yunnan, Xinjiang and Xizang formed three separate clades. We suggested that these species belong to three different genera such as Cyrtodactylus, Cyrtopodion and Mediodactylus. (3) The results did not support the phylogenetic hypothesis of subfamily Teratoscincinae because the Teratoscincinae species embedding in the subfamily Gekkoninae. (4) With support from morphological and genetic distance, we confirmed Gekko houkouensis as a valid species, and its relationship is closer to G. swinhonis than to G.japonicus. (5) The genus Gekko is not a monophyletic group because Gekko gecko divided from the genus and formed a monophyletic clade. Its genetic relationships with other geckos were far (the genetic distance is up to 33.5%) . The G. gecko，therefore, should be considered as a new genus—Gigagekko. (6) The Gigagekko(Gekko) gecko clade divided into four groups. The genetic distances between group I and group II was 11.6%; and 4.6% between group III and group IV. All other pairing were greater than 17.0%. This demonstrated that G.(G.)gecko had differentiated to at least two species or subspecies. Combined with geographic distribution of G.(G.)gecko, there is a transitional zone between China and Southeast Asia. The transitional zone is Wenshan border of Yunnan China-Vietnam border near Guangxi and Northern area of Vietnam. (7) Hemidactylus stejnegeri collected from Taiwan Province (TW01, TW03) was clustered with H. garnotii and their genetic distance was only 0.7%. Combined with the morphological characteristics, H. stejnegeri and H. garnotii are very similar. So we speculated that H. stejnegeri and H. garnotii are synonyms or H. stejnegeri is one of H. garnotii subspecies based on the phylogeny, genetic distance and morphology.
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