In the systematics of cnidarians, the different types of cnidocysts are considered an important taxonomic character. In Hydra, the four types of cnidocysts found in the ectoderm, concentrated in tentacles and their measurements, together with other morphological and reproductive characteristics, are very important for the taxonomy of the species. In this study, we explore in detail the biometric and statistical characteristics of the cnidome of three species of Hydra collected in three different environments for each climate season. A total of 17,378 capsules were measured. We used ANOVA test and Generalized Linear Model to analyze the distribution and differences reflected in each cnidome, considering the factors “individuals”, “season”, “lagoon” and “species”. The results were clear: the cnidome keep specific information that, together with other taxonomic characteristics, allows us to discern between species of different groups. The same happens with cnidome of the same species but from different lagoons or climatic seasons: we observed a variation of parameters for each type of cnidocyst that could differentiate “ecological races”, since these differences are not enough to declare different species.