Populations of blue-tongue skinks inhabiting eastern Wallacea and New Guinea are traditionally assigned to either Tiliqua gigas, which is endemic to this area, or to Tiliqua scincoides that extends its range from the Australian continent. Despite a wide morphological variation among local populations, genetic data from non-Australian populations were almost absent. We examined 128 specimens and sequenced mitochondrial ND4, 12rRNA and nuclear cmos genes. A phylogenetic analysis revealed the presence of two main clades corresponding to species Tiliqua scincoides and Tiliqua gigas. We provide the first report of Tiliqua scincoides from the Aru Island and confirm that it is genetically related to the Tanimbar populations reported as Tiliqua scincoides chimaerea. The other samples belonged to Tiliqua gigas, which also shows a distinct phylogenetic structure congruent with the geographic origin of the samples. The main split conforms to the north-south pattern of genetic variation, which was also reported in other animal species in New Guinea. (1) Samples from the northern coast of Irian Jaya, Seram, and Kai Islands belong to a distinct clade, which further splits supporting the recognition of the Tiliqua gigas keyensis subspecies. (2) Samples from the Bird’s Head and southern coast of the Irian Jaya and Halmahera Island form the other clade within Tiliqua gigas, in which the Halmahera samples formed a shallow, but clearly distinct branch. The haplotype network analysis of mitochondrial ND4 gene in Tiliqua gigas samples suggests a strong differentiation among major population groups.

传统上，居住在华莱士东部和新几内亚的蓝舌石龙种群被分配到该地区特有的Tiliqua gigas，或延伸到澳大利亚大陆以外的Tiliqua scincoides。尽管当地人群的形态差异很大，但几乎没有来自非澳大利亚人群的遗传数据。我们检查了128个标本，并对线粒体ND4、12rRNA和核cmos基因进行了测序。系统发育分析表明，存在两个主要进化枝对应的物种为Tiliqua scincoides和Tiliqua gigas。我们提供了Tiliqua scincoides的第一份报告来自阿鲁岛（Aru Island）的物种，并证实它与报道为Tiliqua scincoides chimaerea的Tanimbar种群遗传相关。其他样品属于Tiliqua gigas，也显示出与样品的地理起源一致的独特的系统发育结构。主要的分裂符合遗传变异的南北模式，新几内亚的其他动物也有报道。（1）来自Irian Jaya，Seram和Kai群岛北部海岸的样本属于一个独特的进化枝，进一步分裂后支持对Tiliqua gigas keyensis亚种的识别。（2）鸟头和Irian Jaya和Halmahera岛南部海岸的样本构成了Tiliqua gigas内的另一个分支，其中Halmahera样品形成了一个浅而清晰的分支。Tiliqua gigas样品中线粒体ND4基因的单倍型网络分析表明，主要人群之间存在强烈的差异。