A species complex exists in all groups of organisms where two or more organisms that are closely related have similar appearance and are not completely differentiated between one another because of the lack of evidence and data. The latest discovery of a new species of tree frogs, Polypedates discantus in Thailand proves that further research is needed to uncover and unveil certain species complex under Polypedates leucomystax. This would ultimately avoid local and global species diversity from being underestimated. The aim of this study was to determine whether Polypedates discantus of peninsular Malaysia can be separated from Polypedates leucomystax of Malay Clade by using morphometric analysis. Samples of adults Polypedates leucomystax were collected from several locations in peninsular Malaysia particularly Perak, Kelantan and Pahang. The samples were then preserved in 70% ethanol solution and its morphological measurements were measured using a vernier caliper. Data collected is analyzed using PAST analysis software version 3.25 where it undergoes data confirmation, multivariate analysis and species conformation according to the discriminant function analysis chart given. The expected results of this finding will produce different clusters between the two species population of Perak, Kelantan and Pahang. Thus drawing a dividing line between the two species which will have a huge impact on conservation biology.