Isopods, characterized by direct development, lack a planktonic stage that would allow for long-distance dispersal. For some herbivorous species, though, rafting on floating macrophytes (including seaweeds) could be a mechanism to facilitate population connectivity over wide distances. In addition, the phylogeography of these species is expected to be related to that of their dispersal vectors. In the current study, we sequenced a fragment of 636 bp of the COxI gene in 107 individuals of the kelp-dwelling isopod Amphoroidea typa from ten populations along 2500 km of the Chilean coast (27 degrees S - 43 degrees S); no isopods were found at two sites in northern Chile (21 degrees S and 23 degrees S). Our results reveal the existence of population genetic structure and isolation by distance in A. typa. We identified three geographic groups: one represented by the four northernmost populations (27 degrees 32 degrees S), a second one including two central populations (34 degrees-37 degrees S), and the last one comprising the southernmost populations (39 degrees-43 degrees S). These results are partially explained by the effect of El Nino, which enhances extinction and recolonization of kelp forests and associated grazers north of 30 degrees S. The results show that A. typa does not have any specific kelp preferences and dwells on kelp species with different dispersal capabilities, such as the non-buoyant Lessonia spp. and the floating giant kelp Macrocystis pyrifera. Individuals of A. typa appear capable of switching between different kelp hosts during their lifetime, including vectors that permit rafting over long distances, and thereby contribute to population connectivity throughout the distribution range of this herbivorous isopod. The main outcomes of the current study support the idea that organisms dwelling on positively buoyant macrophytes can effectively disperse together with their floating hosts.