The taxonomy of four isolated strains of Anabaenopis elenkinii and A. arnoldii from North and South America were investigated using a polyphasic approach. The studied populations were collected from seven alkaline lakes of the Brazilian Pantanal and Nabor Carrillo Lake, Texcoco region (Mexico), between 2004 and 2012, where they frequently formed blooms during the dry season. The morphological plasticity of the populations, from natural and culture conditions, was described based on 200 individuals of each species. The 16S rRNA and the cpc-BA-IGS phylogenetic analyses show Anabaenopsis as a sister-taxon of Cyanospira. The Anabaenopsis clade has three strongly supported subclusters related to the origin of strains: Pantanal+Mexico, Kenya+Australia and one European clade. Although these data indicate that the currently known Anabaenopsis strains belong to more than one species, we are being conservative and not describing them as new species due to the lack of more molecular data. We highlight the need of a revision of the genus, considering also that Anabaenopsis sp. PCC 9215, the current reference strain used for the genus, is not identified as A. elenkinii and it is phylogenetically grouped with Anabaenopsis strains identified as A. circularis, A. arnoldii, A. nadsonii and A. elenkinii.