Freshwater prawn Macrobrachium rosenbergii (De Man, 1879) is one of the most economically important crustacean species cultured within its' natural distribution and beyond. In Sri Lanka, Macrobrachium rosenbergii has gained a value as an important organism in aquaculture. In culturing programs, brood stocks are collected from the wild populations. Thus, wild stocks are important as an immediate resource for addressing diversity problems in cultured stocks. This study analysed intraspecific variation among four populations of M. rosenbergii using morphological data. Samples were collected from four localities (populations): Negombo lagoon, Bolgoda estuary, Walawe River estuary and Nilwala River estuary. Total of 179 individuals were analysed using 10 morphometric and 2 meristic parameters. To determine the significant difference of size standerdized morphometric parameters among four populations, One way analysis of variance (ANOVA) was used. To distinguish four populations, Discriminant Function Analysis (DFA) was performed using morphometric parameters. First two discriminate functions totally accounted for 88.9% (69.3% and 19.6%) variables. First discriminate function by itself identified nine morphometric characters as contributors for this analysis. According to the results of ANOVA, all morphometric characters were variable among four populations which indicated the availability of adaptive traits within the species. However, Discriminant Function Analysis failed to distinguish geographically separated four M. rosenbergii populations. The importance of collecting information on population diversity levels of economically valuable aquatic species when constructing aquaculture and conservation programs are discussed.