Giant freshwater prawn, Macrobrachium rosenbergii is known to be the largest palaemonid in the world. It is important crustacean species that distributed not only within its natural range, but even beyond. Identification of geographically diverse M. rosenbergii populations is important as the broodstocks are selected from wild populations in culturing programs. The morphological differences among geographically different populations may be attributed to the distinct genetic structure and environmental condition. Thus, this study is carried out to analyse the morphological of 81 individuals of M. rosenbergii from Kelantan, Perak and Sabah based on morphometric and meristic parameters. Besides, the present study had also reviewed the genetic data made by previous researchers to relate with the morphological variability among the populations. One way analysis of variance (ANOVA) was used to determine the significance difference of morphometric and meristic parameters among three populations. Discriminant Function Analysis (DFA) was performed on the morphometric parameters to identify main characters to differentiate the studied populations. Result founds that the most reliable character to differentiate within populations is abdominal length while Sabah population showed high morphological differentiation compared to Kelantan and Perak. There are significant variability within morphological and genetic characteristics among studied populations. Local adaptation, existence of geographic barriers, high water salinity and current flow pattern promote significant variability between Populations. Information from the present study might be useful for conservation programme, future researches and improving the freshwater prawns industry as M. rosenbergii is one of the indigenous species in Malaysia.