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<i>Microcystis</i>-dominated blooms cause environmental and ecological impacts worldwide. However, it is sometimes challenging to correctly identify <i>Microcystis</i> and its related genera. <i>Radiocystis fernandoi</i> Komárek et Komáková-Legnerová 1993, characterized by large cells and correspondingly large colonies with gas vesicles, has been frequently found in cyanobacterial blooms in Brazil. However, its molecular and phylogenetic identity is unknown because no valuable DNA sequences are available in GenBank. In this study, a strain with <i>R. fernandoi</i> morphology was successfully isolated from a cyanobacterial bloom sample in Lake Erhai, a subtropical plateau lake in China. Molecular characterization and phylogenetic analyses based on 16S rRNA and <i>cpc</i>BA genes revealed that the strain is different from the type species of the genus <i>Radiocystis</i> but formed a well-supported clade with the <i>Microcystis</i> species. The comparative results of the ITS region between 16S–23S rRNA genes also showed that the strain had very similar secondary structures to the species of <i>Microcystis</i>, supporting it as a new member of the genus <i>Microcystis</i>. Therefore, we propose the transfer of <i>Radiocystis fernandoi</i> into <i>Microcystis fernandoi</i> comb. nov. The correct identification and further taxonomic procedure for the bloom-forming cyanobacterial genera, such as <i>Microcystis</i>, <i>Radiocystis,</i> and <i>Sphaerocavum</i>, are also discussed in this study.