Three strains of Limnothrix (Cyanobacteria) isolated from Lake Kastoria, Greece, were characterized based on their morphological features and 16S rRNA gene sequences. The Limnothrix isolates 007a, 165a, and 165c can morphologically be assigned to Limnothrix redekei (Van Goor) Meffert. The 16S rRNA gene of the Limnothrix strains showed a 99% similarity to the 16S rRNA gene of Planktothrix sp. FP1. Limnothrix redekei strains 165a, 165c, 007a and Planktothrix sp. FP1 formed a separate cluster in the cyanobacterial 16S rRNA gene tree. It was distinct from the Pseudanabaena cluster, which included the other Limnothrix strains isolated from northern temperate lakes. This is the first report on the phylogeny of L. redekei strains originating from a Mediterranean lake (southern Europe) and provides new data about the genus Limnothrix.