This study explores the use of a long fragment of the mitochondrial cytochrome oxidase subunit 1 (CO1) marker to elucidate the genetic diversity of Aedes albopictus sampled from urban and forested regions in Peninsular and East Malaysia. A total of 36 samples were collected from 5 localities from which its genetic variability was analysed. 33 distinct mtDNA haplotypes were identified following the amplification and sequencing of the concatenated CO1 gene. The analysed region of the CO1 gene identified substantial levels of genetic diversity among mosquitoes in urban populations and revealed unique genealogical relationships between local isolates as revealed in the haplotype network. This study highlights the reliability of the long CO1 fragment to identify genetic divergence of Aedes albopictus which can be utilized in forthcoming studies.