In shallow sublittoral rocky habitats of the Southeast Pacific, two conspicuous ecological systems exist kelp beds dominated by large Laminariales algae, and barren grounds dominated by crustose coralline algae and sea urchins. The aim of this study was to examine the successional development of micro-periphyton communities in both ecological systems using a colonization experiment conducted in Northern Chile. In both ecological systems, we installed replicated ceramic plates at 10 m depth and samples were taken after 1, 2, 4, 6, 8 and 14 days of exposure. Bacteria, diatoms, protozoans and small eukaryotes were identified, quantified and analysed. The succession of micro-periphyton communities in both ecological systems followed a common pattern consisting of a net accumulation of functional groups and taxa over time; however, the total density of all groups was significantly higher in the kelp beds. In addition, the community structure of the developing micro-periphytons was different and specific for each ecological system. Although previous studies have suggested that kelp beds and barren grounds are capable of switching from one state to the other without substantial changes in biodiversity, our results show that each of these ecological systems promotes its own successional development, suggesting that they are unique, self-organized entities. This study is the first step towards an understanding of these ecological systems operating independently at this scale of organization.