Geometric morphometric analysis recently has expanded to insects of forensic importance, mainly adult flies, as correct and valid species identification is important in forensic entomology. The objective of this research was to investigate morphological variations between two forensically important scuttle flies (Diptera: Phoridae) in Malaysia, i.e. Megaselia scalaris (Loew, 1866) and Megaselia spiracularis Schmitz, 1938, based on wing shape analysis. A total of 16 geometrical landmarks was defined and analysed with geometric morphometric procedures using MorphoJ software. Wing centroid size, which represented wing shape, was statistically different between species and sexes. By using residuals from the allometric effect, canonical variate analysis separated all defined groups in different distinct clusters and further cross validated by both species and sexes. Between species, male M. scalaris had broader wing shape than male M. spiracularis, whilst in the female, M. scalaris had a narrower shape at the tip of the wing. Within M. scalaris group, females had broader wing shape at the base than males, whereas in M. spiracularis, the females had narrower shape at the base of the wing than the males. The geometric morphometric analysis in distinguishing forensically important species could be expanded for further investigation, especially in Phoridae family.