Cyanobacteria belonging to Nostocales family are a highly diverse group in relation to form, function, and habitat. Current cyanobacterial systematics relies on the observation of flexible morphological characters. Accurate and reliable delineation of Nostoc sp. has not been possible by traditional methods. Phylogenetic studies of Nostoc sp. based on morphological and physiological observations have demonstrated the conflicts in identification and genetic relationships among the Nostocacean strains. Therefore, supplementary genetic information should be incorporated to give a polyphasic classification system for the order Nostocales. In the view of above, the current investigation on the molecular and phylogenetic characterization of three species of the genus Nostoc based on cpcB-IGS-cpcA locus of the phycocyanin operon was carried out. The phylogenetic position of these species within order Nostocales had been determined. The results indicated that genus Nostoc is heterogeneous. Analysis of the IGS region between cpcB and cpcA showed that Nostoc and Anabaena are distinct genera, while the taxonomic status of the genera is still unclear. These data indicated that additional analyses and revision of the taxonomic position of Anabaena, Anabaenopsis and Nostoc species within Nostocales are required.