Diversification of morphological characteristics among geographically separated populations is particularly important in understanding evolutionary processes and is considered the early stage of allopatric speciation. In the present study, we investigated geographic variation in scorpion populations of Bothriurus bonariensis (Koch 1842). Our principal goal was to compare different populations of this species with regard to its distribution, analyzing somatic and genitalic characters. In Argentina, specimens of B. bonariensis from Entre Ríos and Corrientes Provinces are dark brown, while specimens from La Pampa have reddish coloration. Scorpions of this species from Brazil and south of Uruguay are totally black. Also, we observed variability in body size, some morphological characteristics of adult specimens (e.g., prosoma length, hand height, hand width, and telson height), and genitalic traits (e.g., hemispermatophore lamina length, basal and distal lamina width, dorsal fold length). Results indicate the presence of evident geographic variation: populations from Argentina show similar morphological patterns that differ from populations from Uruguay. We discuss these data in the context of the current phylogeographical and evolutionary knowledge of this species.