Morpho-functional polymorphism of modules, also known as “division of labor”, is a widespread phenomenon independently evolving multiple times in the colonies of many aquatic invertebrates and invertebrate chordates. Polymorphic zooids are especially diverse among Cheilostomata, the evolutionarily most successful clade in the phylum Bryozoa. The most diverse among cheilostome polymorphs are avicularia and vibracularia, acting as defensive, repelling, cleaning and locomotory “colonial organs”. While their skeletal characters were intensively studied, the soft tissues have largely been neglected. This hampers evolutionary interpretations. In this study, we compared the muscular system in five contrasting types of these polymorphs from 10 species of eight related as well as distant families. In contrast with the prevailing view, we found that the structural and functional changes affecting the muscular system during evolutionary transition from autozooid to polymorph were considerably more diverse and complex than mere “vestigialization”. These changes included muscle loss, hypertrophy, rearrangement (regrouping and relocation), fusion, and acquisition of asymmetry and muscle striation. Asynchronous contraction of originally synchronously working muscles was presumably evolved in advanced vibracularia. Some of these modifications were recorded in all avicularian types, whereas others were characteristic only for particular taxa or polymorphic categories. Our study showed that not only skeletal, but also soft parts of the polymorphs were evolutionarily very flexible and modified to various degrees and in various directions.