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One of the interesting (main) questions concerning evolution of the organisms is the revealing of the mechanisms underlying evolutionary changes in organisms. Possible explanations of morphological diversity within a certain taxon are of particular interest. In general, modular organisation implies high diversity of spatial arrangement of main modules within such an organism. Most of the hydrozoans have colonial (= modular) organisation at the polyp stage. In thecate hydroids (Hydroidomedusa, Leptomedusae) the rigid outer skeleton fixes the spatial arrangement of the colony modules allowing detailed analysis of the morphogenetic processes involved on colony growth. In the present essay, we discuss possible evolutionary mechanisms responsible for the morphological diversity of colonies in thecate hydroids. The growth of the thecate hydroids bases on cyclic functioning of the growing tips shaping new colony modules. The primary morphogenetic cycle starts with emergence of the new growing tip, passes though development of the internode and ends with differentiation of a hydranth. It looks like that the stolon growing tip functions in acyclic mode, but we provide the evidence that such mode evolved from the cyclic one due to the heterochrony. That is the next stolon growing emerges before the existing tip starts differentiation into the hydranth. Allometry in growth of modules underlies the evolutionary and ontogenetic changes in spatial organization of shoots in colonies of thecate hydroids. Disproportionate enlargement of the rudiment during module development creates the prerequisites for earlier emergence of the next the growing tips (heterochrony). Earlier emergence of the next growing tips allows morphogenetic integration of several “primary” modules into “secondary” ones. That leads and in certain cases determines changes in mutual spatial arrangement of primary modules (heterotopy). In many cases, these changes can be traces in the ontogeny of a single hydroid colony with complex organization.