A series of meromictic lakes, stratified fjords and freshwater lakes at the northern limit of the Canadian High Arctic (northern coastline of Ellesmere Island, Nunavut) were sampled at different depths to quantify the presence of cyanobacteria and to describe their molecular diversity. The sampled ecosystems spanned a wide span of physico-chemical conditions, with conductivities ranging from freshwater (0.2 mS . cm –1) to seawater (48 mS . cm –1) and temperatures rang-ing from – 1.91 to 12 °C. Fluorescence microscopy cell counts showed that picocy-anobacteria occurred in high concentrations (10 3 to 2.5 x 10 4 cells . ml –1) in the oxic and suboxic zones of all of these waters. Molecular analysis of the 16S rRNA gene using Denaturating Gradient Gel Electrophoresis (DGGE) and clone libraries of samples from 8 different lakes and fjords revealed a low diversity of picocyano-bacteria affiliated to the genus Synechococcus. In total, 132 short sequences from DGGE bands, clones and strains were obtained. Most of the sequences (83 %) clustered in two closely related groups that tend to separate according to saline or freshwater conditions. However, some representatives of each OTU were found in different types of habitat, suggesting some degree of tolerance. These results show that picocyanobacteria are widely distributed under a broad range of physical and chemical conditions in the Arctic environment, and that some genotypes may be specialists that occupy specific habitat types.