A limited sampling campaign on the main island of Îles Kerguelen revealed 170 freshwater diatom taxa, belonging to 29 genera. Four different communities were distinguished in two major groups, being determined principally by habitat type. The Fragilaria vaucheriae–Fragilaria germainii assemblage occurs exclusively in running waters. The three other communities, observed in standing waterbodies, are separated by their geographical position on the island with the Fragilaria exigua–Aulacoseira alpigena and the Fragilaria exigua–Fragilaria vaucheriae assemblages, mainly found in the Lac Studer area and the Fragilaria pinnata var. pinnata assemblage, recorded near the coastal line and the research station. Analysis of different waterbody types revealed the habitat preference of the various diatom taxa and identified a diatom flora for running waters and one preferring stagnant waterbodies.