Compromising more than 120 species and found worldwide, Hemidactylus geckos are one of the most diverse and widely dispersed genera of reptiles. Of them the Common house gecko, Hemidactylus frenatus, is one of the most recognized and widely distributed and has invaded the Mediterranean region, Australia, most Pacific Islands, Europe, and North and South America over the past 100 years. Their proposed native range is the source of much controversy and many of their more recent colonizations are theorized to be largely anthropogenic. Here I present a molecular phylogeny for Taiwanese H. frenatus based on 681 bp of mitochondrial DNA (cytochrome b) and 309 bp of nuclear DNA (RAG1) from 19 individuals with the addition of H. bowringii, H. brookii, and H. garnotii individuals as outgroups. Samples from other countries were also obtained from GenBank. Results of phylogenetic analyses revealed two distinct clades, wherein Clade 1 is restricted to India and Southeast Asia while Clade 2 encompasses the same region with additional incursions to the rest of the world. Individuals from Taiwan are represented in both clades. However, Taiwan individuals from the India-SE Asia clade were all collected from a singular locality, lending support to multiple incursion events in Taiwan and a non-native status in Taiwan. As a cryptic species, H. frenatus origins in Taiwan are still difficult to decipher and additional research using molecular markers with a higher mutation rate is needed for further clarity.