Little is known about the extent of the genetic diversity and its structuring patterns in protist species living in lakes. Here, we have investigated the genetic diversity patterns within five dinoflagellate species (Peridinium aciculiferum, Peridinium cinctum, Peridiniopsis borgei, Polarella glacialis, Scrippsiella aff. hangoei) that are present in lakes and sometimes, in marine habitats located in polar and temperate regions. A total of 68 clonal strains were investigated using Amplified Fragment Length Polymorphism (AFLP), a sensitive genetic fingerprinting technique. All used strains within each species had identical ITS nuclear ribosomal DNA sequences, a characteristic that indicates that they likely belong to the same species. We found a wide variability in the genetic diversity among species (between 20% and 90% of polymorphic loci; Nei's gene diversity between 0.08 and 0.37). In some cases, our analyses suggested the presence of different genetically homogeneous subgroups (genetic populations) within the same water body. Thus, it appears that different genetic populations can coexist within the same lake despite the likely occurrence of recombination that tends to homogenize the gene pool. Overall, our results indicated that a large number of dinoflagellate genotypes are present in lake populations, instead of a few dominating ones. In addition, our study shows that protists with identical ITS sequences can harbor considerable amounts of genetic diversity.