Barriers to dispersal are recognized to play an important role in the differentiation of populations and ultimately in speciation. In the southeast Pacific, on the northern coast of Peru, a transition zone between the Peruvian and Panamic marine biogeographic provinces exists. Here, the convergence between two contrasting surface currents could generate a barrier effect for the larval dispersal of meroplanktonic invertebrates, which could in turn generate differentiated populations or genetic lineages on both sides of the transition zone. To address this, we studied to Echinolittorina paytensis, an abundant rocky intertidal periwinkle that spans both biogeographic provinces. A total of 95 individuals from Ecuador (2°19′S) to central Peru (7°31′S), covering the Panamic Province, the Peruvian Province, and the transition zone between, were collected. The mitochondrial markers cytochrome c oxidase I and 16SrRNA were sequenced in order to investigate phylogeography and genetic structuring. In general, no genetic structuring was found across the transition zone, suggesting this biogeographic boundary would not be acting as a barrier in this species. Factors such as a high larval dispersal capability and the occurrence of El Niño–Southern Oscillation events such as El Niño are discussed.