Many factors have contributed to the destruction of fish habitats. Hydroelectric dams, water pollution and other environmental changes have resulted in the eradication of natural stocks. The aim of this study was to detect the genetic variation in Prochilodus marggravii from three collection sites in the area of influence of the Três Marias dam (MG) on the São Francisco river (Brazil), using the RAPD technique. The results obtained revealed that the fish in the downstream region nearest the dam have a higher similarity coefficient than those from the other sampling sites that may be related to differences in environmental characteristics in these regions. Additionaly, significant differences in the band frequencies were observed from one collection site to another. These both findings suggest the occurrence of a structured population and have important implications for the conservation of the genetic variability of distinct natural P. marggravii stocks
