We used amplified fragment length polymorphisms (AFLPs) to conduct a study of the genetic diversity of Flemish populations of Iris pseudocorus in two hydrologically isolated river basins. AFLP analysis using four primer combinations was carried out on 88 different ramet samples, collected at nine different locations. A total of 148 polymorphic markers were scored. Samples from the basin of the Ijzer river were different from those of the basin of the Scheldt river, require can be explained by the geographical and hydrological isolation of both the basins. A high degree of genetic diversity was detected in the Populations, although the AFLP technique allowed us to identify three ramets belonging to one clone. The different genetic background in the basins of the rivers Ijzer and Scheldt enforce the use of local material in re-plantation projects for the conservation of natural genetic resources of yellow flag in both the basin. (C) 2002 Elsevier Science B.V. All rights reserved.