a b s t r a c tThe increase in resistance to contaminants can result in the loss of genetic diversity of impacted populations. In this work, the effects of acid mine drainage (AMD) on the genetic diversity and structure of a historically exposed population of Daphnia longispina were evaluated using amplified fragment length polymorphism (AFLP) analysis. Individual sensitivity to acute copper exposure was determined in order to characterize the populations in terms of metal tolerance and in an attempt to identify possible contaminant indicative bands (CIB). No reduction in genetic diversity was found in the AMD impacted site population, in comparison to two reference populations. However, the analysis of molecular variance indicated a significant genetic differentiation from the two reference populations and a significant correlation between individual genetic distance and tolerance. The different average tolerance of individuals presenting one specific AFLP band indicated the existence of one putative CIB.