Aedes albopictus is a native mosquito to Southeast Asia with a high potential for disease transmission. Understanding how Ae. albopictus populations that develop in the species’ native range is useful for planning future control strategies and for identifying the sources of invasive ranges. The present study aims to investigate the genetic diversity and population structure of Ae. albopictus across various climatic regions of Vietnam. We analyzed mitochondrial cytochrome oxidase I (COI) gene sequences from specimens collected from 16 localities, and we used distance-based redundancy analysis to evaluate the amount of variation in the genetic distance that could be explained by both geographic distance and climatic factors. High levels of genetic polymorphism were detected, and the haplotypes were similar to those sequences from both temperate and tropical regions worldwide. Of note, these haplotype groups were geographically distributed, resulting in a distinct population structure in which northeastern populations and the remaining populations were genetically differentiated. Notably, genetic variation among the Ae. albopictus populations was driven primarily by climatic factors (64.55%) and to a lesser extent was also influenced by geographic distance (33.73%). These findings fill important gaps in the current understanding of the population genetics of Ae. albopictus in Vietnam, especially with respect to providing data to track the origin of the invaded regions worldwide.