Among anthropogenic habitats built in the marine environment, floating and nonfloating structures can be colonized by distinct assemblages. However, there is little knowledge whether these differences are also reflected in the functional structure. This study compared the functional diversity of sessile and mobile invertebrate assemblages that settle over 3 months on floating vs. non-floating artificial habitats, in two Chilean ports. Using morphological, trophic, behavioral, and life history traits, we found differences between mobile and sessile assemblages regarding the effect of the type of habitat on the functional diversity. Compared to sessile assemblages, a greater functional similarity was observed for mobile assemblages, which suggests that their dispersal capacity enables them to balance the reduced connectivity between settlement structures. No traits, prevailing or selected in one or the other habitat type, was however clearly identified; a result warranting for further studies focusing on more advanced stages of community development.