Macrobrachium Bate, 1868 is the most speciose genus of the family Palaemonidae. Among these, the neotropical species Macrobrachium amazonicum (Heller, 1862) is considered as particularly successful, showing an extremely wide range of distribution (ca 4.000 km across). Populations assigned to this species live in estuaries along the northern and northeastern coasts of South America as well as in fresh water habitats in the Amazon, Orinoco and Paraná-Paraguay river basins. Following recent comparative studies that showed differential ecological, reproductive, developmental and physiological traits in geographically separated populations from the Amazon delta and the Pantanal region, Brazil, we examined the morphology and morphometry of adult shrimps from these two regions. Based on significant differences, we conclude that the Pantanal population constitutes a new species, which is described here as Macrobrachium pantanalense. The main morphological differences between M. amazonicum and the new species have been found on the second pereiopod and on the telson of both males and females, moreover in the maximum size of females vs. males.