Morphological traits that appear multiple times when mapped onto molecular phylogenies have been associated with character lability. In an ecological context, functional characters, if labile, could confer advantages for adaptation to specific habitats. Bamboo corals are long-lived, deep-sea octocorals characterized by an obvious modularity, which affords diverse branching morphologies in the Keratoisidinae subfamily. We reconstructed molecular phylogenies using 16S (mitochondrial) and ITS2 (nuclear) ribosomal DNA, and obtained 39 ITS2 and 22 16S sequences from 22 different specimens. The molecular topologies showed Keratoisidinae genera as polyphyletic. Twelve morphological characters were chosen to make the ancestral character reconstruction, none of which exhibited character states forming monophyletic groups when mapped onto molecular phylogenies. The different character states appeared as having been gained and lost multiple times. Modular organisms such as bamboo corals could have higher character evolvability than unitary organisms. Complexity arising from simple body plans is a typical characteristic in most modular organisms, such as plants and colonial marine invertebrates. However, bamboo corals may also exhibit phenotypic plasticity associated with continuous characters, given that they can respond to extrinsic controls. Our results also have direct repercussions on Isididae taxonomy, since morphological characters have been used for their classification. Consequently, we suggest that the current taxonomy of the group is re-evaluated and that the different mechanisms regulating modularity and character evolution in bamboo corals are explored.