Traditional cyanobacterial taxonomy is usually confusing and complicated. The genus Microcystis, considered as one of the most relevant planktonic organisms from an ecological (cyanobacterial blooms development) and public health (hepatotoxin production) point of view in continental waters, exhibits an extremely difficult species identification, especially due to the morphological variations that frequently occur in definable and recognizable phenotypes (morphospecies). Consequently, the study of Microcystis morphospecies variability and definition of their morphotypes will contribute to improve morphological delimitation and thus species recognition within this genus. Several species of Microcystis, including M. aeruginosa, M. flos-aquae, M. novacekii, M. viridis and M. wesenbergii, were identified in a eutrophic reservoir from Madrid (Spain). Isolation of strains belonging to these morphospecies allowed development of the morphotypes in culture and their morphological characterization. The comparison between field and cultured colonial forms was carried out and the corresponding taxonomic implications were explored. Identified morphospecies suffered, under culture conditions, morphological variations leading to colonies different to those from the initial morphotypes, as well as colonial characteristics typical of other morphospecies. Main variations were seen in M. aeruginosa, M. flos-aquae and M. novacekii strains, where new morphotypes are defined. Microcystis aeruginosa and M. novacekii isolates shared similar morphologies that would undoubtedly make their successful identification difficult if they were observed in field samples. Despite variations, the rest of the isolates conserved enough morphological features to allow their correct morphospecies assignation. A hypothetical developmental sequence of morphotypes for M. novacekii is proposed based on colonies observed in culture over time.