Biogeography, phylogeography and ecology of the diverse assemblage that inhabits the south-east Pacific along the Humboldt Current system (HCS) has received increasing attention. Regions separated by biogeographic break evidence changes in the functional structure of consumer assemblages, likely related to a replacement from tropical to temperate species. The deep temporal signature of coastal oceanography on coastal biogeography and phylogeography is underpinned by the spatial structure of bottom-up effects of ecological processes, which also influence the strong top-down regulation of consumers on the structure of rocky shore communities. Uncertainties still remain about how coastal oceanographic processes regulate species range expansion/contraction and how biotic interactions and environmental filtering define dynamic biogeographic patterns along marine environments. Explicit predictions should be made regarding the persistence and dynamics of species ranges, and changing ecological interactions among species in the face of intensified human harvesting (e.g., kelps) and global change. Clear cooling trends are observed across the HCS, human harvesting is intensifying and presence of coastal artificial infrastructure could trigger species range shift. Aquaculture expansion and the introduction of exotic non-native species have the potential to alter community structure and functioning. Hence, ecosystem services should be managed, and necessary interventions carefully planned to ensure sustainability of use of natural marine resources and coastal ecosystem integrity.