Abstract: Indonesia has two species of indigenous freshwater prawn Macrobrachium rosenbergii and Macrobrachium idae which are distributed in different environments/habitats. Adaptation to different environments leads to dissimilar characters, causing morphological variance which could be evaluated using morphometric character measurements. This study was aimed to discover the morphometric variation of the population of freshwater prawn Macrobrachium rosenbergii and Macrobrachium idae in South Sulawesi. The samples were taken from Waelawi River in North Luwu, Kariango River in Pinrang and Tempe Lake in Wajo. The freshwater prawn’s morphology was analyzed descriptively based on the coefficient of variance. The Macrobrachium rosenbergii’s coefficient of variance was relatively high, ranging between 9.33% and 71.20% and the coefficient of variance for Macrobrachium idae was between 8.69% and 67.49%. The analysis of 25 morphological characters demonstrated that the population was heterogeneous, which was probably caused by difference in habitat.