We investigated to what extent DNA-markers can assist species determination in the genus Typha. A set of AFLP markers was used to discriminate samples of the species Typha latifolia and Typha angustifolia collected in Flanders (North Belgium). The T latifolia samples formed a compact cluster while the T angustifolia samples were divided into smaller groups. It was not clear whether interspecific hybrids or higher levels of diversity present in the T angustifolia dataset could account for this. As in previous surveys, using isozyme and VNTR markers, AFLP markers revealed an almost complete lack of genetic variation in Flemish T latifolia. Despite the low degree of diversity, a significant level of genetic differentiation was found between the T latifolia samples originating from different river basins. Whether this differentiation has any ecological relevance remains to be investigated. The methodology applied was not able to detect clonal reproduction in T latifolia. Probably, the low levels of diversity present in this species can account for this, indicating that the usefulness of the methodology applied depends on the level of diversity present in the species studied. (C) 2005 Elsevier B.V. All rights reserved.