Echium vulgare L. (Boraginaceae) is a tetraploid pseudometallophyte plant commonly occurring on dry, coarse textured soils as well as on heavy metal contaminated substrates. In the present study, the genetic diversity and differentiation of two populations of E. vulgare originating from ZnePb mining and smelting waste deposits (MP, MB populations) and one from uncontaminated soil (NM population) were examined. Patterns of genetic variability within and between the populations were assessed using three molecular marker systems e inter simple sequence repeat (ISSR), amplified fragment length poly-morphism (AFLP), and simple sequence repeat (SSR). Our results showed that severe environmental conditions did not reduce the genetic diversity (no bottleneck effect) but increased it. All markers except for AFLP indicated differentiation between metallicolous and nonmetallicolous populations. The molecular marker systems used did not provide uniform information concerning intra-and interpopulation diversity of E. vulgare; therefore , using a single technique only instead of a combination of a few marker systems may give misleading results.