Metisa plana Walker, has contributed as an important pest in the palm oil industry. Even though various studies have been conducted on M. plana there is still insufficient information on the relationships among the populations to illustrate the distribution of this species. We aim to investigate the phylogeography of the M. plana populations by combining data of cytochrome c oxidase subunit I (COI), cytochrome b (Cytb), and 28S markers. The M. plana specimens have been sampled from 10 heavily infested oil palm plantations in Peninsular Malaysia. A total of 145 sequences of three markers were combined and implemented for the phylogenetic analyses, Neighbour-Joining (NJ) and Bayesian Inference (BI). Both phylogenetic trees showed mixing of individuals of the M. plana inter-populations, despite a very distinct geographical isolation. Based on findings from the haplotype analyses; haplotype diversity (Hd= 0.96089), haplotype number (27), haplotype network, and haplotype tree; all supported the genetic exchange, indicating the possibility of gene flow. The genetic exchange occurs probably due to the flying ability of the male moth or caused by the human activities between the various plantations that accidently resulted in the transportation and movement of the pest larvae. Interestingly, the haplotype network has also been visualised in estimating the origin of the infestation, which most probably originated from three different plantations, resulting in the rapid outbreaks of the M. plana infestation. These fundamental data are very crucial and informative in the effort to strategise the management control of the M. plana.