In order to examine how substratum colonisation can affect community structure, a 1-year study was conducted at the Faro/Ancao artificial reef (Algarve, Portugal). In the study of hard substratum communities, motile species are usually neglected and only the conspicuous species are taken into account. Therefore, the development of vagile and sessile components of the epibiotic community were analysed separately. Differences between assemblages on horizontal surfaces, but not on vertical surfaces, were detected. Multivariate analysis detected differences in macrobenthic community structure either considering sessile or motile components. However, significant differences were only detected for vagile fauna. Moreover, this study suggests that for hard substratum communities, analysis of the vagile fauna is important and should be taken into account in the functioning of the artificial raft.