The main element to assess the potential risks associated with toxic cyanobacterial blooms is the precise identification of the species. As part of a water quality monitoring during 2015 in Santa María del Oro crater lake, Nayarit, a cyanobacterial bloom was detected. Thus, this work aimed to identify the bloom-forming cyanobacteria species using a polyphasic approach. The cyanobacteria that produced the bloom were Limnoraphis robusta, which represented the first record for Mexico, and Microcystis aeruginosa, which is a new record for Nayarit. During the bloom’s most intense phase in March and April, the filament and trichome width of L. robusta decreased by 50%, thus, resembling L. hieronymusii morphometry. Despite morphological variations, ecological and molecular data allowed us to assign, unambiguously, the morphotype to L. robusta. According to our data, it is important to trace the cell size of natural populations to assess their morphological variation limits.