In the morphospecies Mazzaella laminarioides, a red alga commonly found along Chilean rocky coasts, three genetic lineages, named North, Center, and South, presenting distinct levels of genetic divergence, have been previously described based on sequences of rbcL and COI. Here, we present the results obtained for six nuclear microsatellites and the COI data acquired for 29 localities positioned between 28°S and 43°S, which allow us to characterize the genetic structure of the species with high resolution and to delimit, for the first time, the transition zones between the three lineages. Our results reveal clearly defined boundaries between the lineages, as well as a marked substructure within each of them. The transition zone between the Northern and Central lineages is located in a narrow transition around 32°48′S, where dispersal appears to be restricted to very local scales, with no evidence of isolation by distance (IBD). At the same time, a mosaic of Center and South sampling sites is observed in an area extending over some 225 kilometers between 37°S and 38°S. None of the four transition zones include sites that can be defined as a true contact zone, an area where two genetic groups are found in sympatry. Population admixture estimated with STRUCTURE detected only a few introgressed individuals even when genetic groups are located a few kilometers apart. We propose that transitions between lineages reflect a combination of historical events and contemporary factors that have persistently limited gene flow along the Chilean coast. In particular, the transition at 32°48′S (not necessarily associated with obvious physical barriers, such as estuaries or sandy beaches) could represent a historical genetic break that has been maintained by current hydrodynamic conditions. In contrast, the mosaic Center-Sur area at 37°S-38°S could be the product of earthquakes, coastal uplift, and subsequent recolonization events.