Multiple clonal isolates from a geographic population of Alexandrium tamarense (M. Lebour) Balech from the North Sea exhibited high genotypic and phenotypic variation. Genetic heterogeneity was such that no clonal lineage was repeatedly sampled according to genotypic markers specified by amplified fragment length polymorphism (AFLP) and microsatellites. Subsampling of genotypic data from both markers showed that ordination of individuals by pair-wise genetic dissimilarity indices was more reliable by AFLP (482 biallelic loci) than by microsatellites (18 loci). However, resulting patterns of pair-wise genetic similarities from both markers were significantly correlated (Mantel test P < 0.005). The composition of neurotoxins associated with paralytic shellfish poisoning (PSP) was also highly diverse among these isolates and allowed clustering of toxin phenotypes based on prevalence of individual toxins. Correlation analysis of pair-wise relatedness of individual clones according to PSP-toxin profiles and both genotypic characters failed to yield close associations. The expression of allelochemical properties against the cryptophyte Rhodomonas salina (Wisłouch) D. R. A. Hill et Wetherbee and the predatory dinoflagellate Oxyrrhis marina Dujard. manifested population-wide variation of responses in the target species, from no visible effect to complete lysis of target cells. Whereas the high genotypic variation indicates high potential for adaptability of the population, we interpret the wide phenotypic variation as evidence for lack of strong selective pressure on respective phenotypic traits at the time the population was sampled. Population markers as applied here may elucidate the ecological significance of respective traits when followed under variable environmental conditions, thereby revealing how variation is maintained within populations.