A significant genetic cline has previously been identified along the Chilean coast in the barnacle Notochthamalus scabrosus. Samples from the previous study, spanning 800 km, were not able to show whether the southern lineage ultimately goes to fixation at higher latitudes. In addition to expanding the geographic sampling of this species, locations that were sampled approximately four to five generations ago were resampled for this study, enabling a temporal comparison of the location and strength of the observed cline. Here, we show that although the cline persists as expected, the tremendous changes in observed lineage frequencies near the clinal boundary are indicative of source-sink dynamics that may be associated with a codistributed biogeographic transition zone. We also find that the southern lineage does not increase in frequency in more southern populations, suggesting that this lineage is maintained through a combination of density-dependent interactions and a coastal fitness gradient.