The sea anemone Condylactis gigantea is an ecologically important member of the benthic community in coral reefs of the tropical Atlantic, and displays two morphotypes with respect to the color in their tentacular tips: the green tip morphotype and the pink/purple tip morphotype. Although some molecular and ecological differences have been found between these morphotypes, no other morphological distinctions have been reported, and currently both are still considered a single taxonomic species. In the present study, we perform an exploration on the variability in the size of cnidae between these two morphotypes and performed statistical analyses to compare the 10 categories of cnidae from specimens hosted in the Cnidarian Collection of Gulf of Mexico and Mexican Caribbean, of the Universidad Nacional Autónoma de México, which were previously collected in several coral reefs localities of the Yucatán Peninsula. Results reveal no significant variation in cnidae size between the two morphotypes, but significant variations were found within each morphotype. In addition, we update the composition of the cnidom of C. gigantea, and the utility of the size of cnidae to distinguish between morphotypes or closely related species is discussed.