AimTrait‐based approaches are powerful to examine the processes associated with biological invasions. Functional comparison among native and non‐indigenous species (NIS) can notably infer whether novel assemblages result from neutral or niche‐based assembly rules. Applying such a framework to biofouling communities, our study aimed to elucidate their distributions within two marine urban habitats (namely floating vs. nonfloating habitats).LocationSoutheast Pacific—Central Chilean coastline.MethodsHere, we examined the distribution of 12 functional traits in fouling communities established on settlement plates, after 3 and 13 months of deployment in the two habitats and across ports in Central Chile. Based upon previously described differences of assemblages and NIS contribution across habitats, we hypothesized that nonindigenous, cryptogenic and native taxon pools would be functionally distinct (and trait biased), and that functional diversity and structure would vary across habitats and successional stages.ResultsOur results show, as anticipated, that nonindigenous (13 taxa), cryptogenic (12) and native (18) taxon pools are functionally distinct, though overlapping in the trait space. Non‐indigenous species are rather related to colonizing traits, while native species are more related to competitive traits. Only one widespread NIS was functionally similar to the late successional and most competitive native species, including taxa elsewhere invasives. Despite differences in taxonomic composition between habitats, we did not observe functional differences between them. In contrast, temporal variations across colonization stages were detected along with an increased contribution in large and long‐lived taxa, together with site‐specific trajectories.Main ConclusionsWe conclude that the functional distinctness among nonindigenous, cryptogenic and native taxa occupying artificial habitats in ports reflects niche‐based processes. Site‐specific trajectories indicate that scale‐dependent assembly processes, such as dispersal and species interactions, are at play.