Sister taxa that have diverged and persisted in sympatry have likely been exposed to the same general environmental changes throughout their evolutionary history and may thus exhibit similar phylogeographies. Here we compare the phylogeographic patterns of two sister species of isopods (genus Tylos) that have broadly overlapping distributions but distinct habitat preferences in the supralittoral zone of Chile. The dynamic geoclimatic history of this region during the Quaternary has been implicated in shaping the evolutionary histories of other coastal taxa. Tylos spinulosus is found at latitudes ~27–30°S and prefers sandy beaches, whereas Tylos chilensis is found at ~27–33°S and at ~39–42°S, but prefers rocky shores. We sampled both species across their ranges and obtained 12S rDNA sequences for 89 individuals of T. chilensis and 40 individuals of T. spinulosus. Additional mitochondrial genes were obtained for a subset of individuals. Despite sharing a most recent common ancestor, similar biology, and a partially overlapping range that presumably exposed them to some of the same major environmental changes during their independent evolution, the two species exhibit strikingly different mitochondrial phylogeographic patterns. Tylos chilensis shows evidence of multiple relatively deep divergence events leading to geographically restricted lineages that appear to have persisted over multiple glaciations. Surprisingly, one lineage of T. chilensis was found in geographically distant localities, suggesting the possibility of human-mediated dispersal. Tylos spinulosus appears to have undergone a relatively recent bottleneck followed by a population/range expansion. Both species show high levels of isolation of local populations, consistent with expectations from their limited autonomous dispersal potential. Consequently, we consider that isolated populations are highly vulnerable to extirpation, and we discuss threats to their persistence, and recommendations for their conservation.