The aim of this study was to clarify the phylogenetic position of the three heterocystous cyanobacteria species Anabaena bergii, Aphanizomenon ovalisporum and Aphanizomenon aphanizomenoides within the order Nostocales. We determined and phylogentically analysed 16S rRNA gene and cpcBA-IGS sequences of four A. bergii, three A. ovalisporum, one A. aphanizomenoides and seven Aphanizomenon sp. strains isolated from Spain, Germany, Israel and Senegal and complemented the analyses with 2 morphometric descriptions of these strains. The phylogenetic clustering did not follow the current botanical classification. All three species clustered separately from the majority of Anabaena and Aphanizomenon strains. A. bergii and A. ovalisporum clustered close to Nodularia, whereas the position of the cluster containing the A. aphanizomenoides strain varied between the trees and the different tree constructing methods used. In addition to A. aphanizomenoides, this cluster contained the two Anabaena species A. kisseleviana and A. oumina. All three species had highly similar DNA sequences at the two fragments analysed and thus, based on evolutionary distances, might be assigned to a single species. Further, our results contradict the previously formulated suggestion that A. bergii and A. ovalisporum are 3 morphotypes of a single species. Instead, A. bergii and A. ovalisporum consistently formed separate clusters, which were less than 96.6 % similar to each other based on 16S rRNA gene sequence analysis. Our results support the idea that the taxonomy of heterocystous cyanobacteria should be revised, but also emphasize the importance of detailed morphological information when molecular data of new strains is used for taxonomy.