Phylogenetic analyses of the Alexandrium tamarense species complex using ribosomal RNA sequences show a differentiation of ribotypes/clades into geographic areas and not into the three morphotypes/species A. tamarense, A. fundyense, and A. catenella. These geographic clades seem to be meaningful in terms of the cell's ability to produce paralytic shellfish poisoning (PSP) toxins: some clades are capable of toxin production whereas others are not. Whereas different parts of the rRNA operon have proven informative in revealing the existence and the relationships of these clades, even internal transcribed spacer (ITS) regions lack the resolution required to gain a deeper insight into the population structure of the species complex. Here the utility of the DNA fingerprinting technique Amplified Fragment Length Polymorphism (AFLP) as a possible tool for such purposes was tested. A mixed sampling strategy was used in order to assess the amount of variation of AFLP banding patterns on the level of populations and geographic clades. Our results suggest that AFLPs can provide useful information at the population level using thorough sampling, whereas the amount of variation found is too high to allow for meaningful comparisons of strains collected from isolated different localities at different time points even though they belong to one geographic clade.