Verrill's modern Mussismilia (the ‘brain corals’) were described in the 19th century, being hitherto considered endemic reef-building species to Brazil. Contrasting with the original diagnoses, highly variable morphological patterns have been observed among the congeners. Interspecific overlapping of major taxonomical characters has resulted in quite inconclusive use of the skeleton macromorphology for the genus. Intending to corroborate the Mussismilia taxonomy, a comparative morphological approach was developed, combining skeleton macro- and micromorphology. A total of 132 colonies was collected between 13°S and 17°S latitude (Mussismilia hispida = 53, Mussismilia harttii = 41, and Mussismilia braziliensis = 38). Qualitative (n = 9) and quantitative characters (n = 7) were selected (the latter was analysed with Kruskal–Wallis and a principal component analysis). A non-parametric test was adopted due to heteroscedasticity and the irregular sampling among populations. As a result, the corallite diameter and number of septa were significantly distinct among the species (α = 0.05). Micromorphology also differs interspecifically, being distribution and size of septal spines diagnostic for the congeners. Intraspecific variation and morphs are approached, ensuring the relevance of the skeleton for the interspecific delimitation and the species identities. Finally, field identification and/or methods based on image analyses from video transects should be adopted with caution. These practices may provide unreliable data, once the information is restricted to the view of the colony top, resulting in biased identification – majorly if the morphotypes of M. harttii and M. hispida share closely spaced corallites.