The scallop Argopecten purpuratus is a heavily exploited resource along the coasts of Peru and north-central Chile, especially after El Niño events, when the species undergoes high increases in abundance. Little is known about its genetic structure or demographic history, two important factors to ensure sustainable exploitation. We sequenced the cytochrome oxidase I and cytochrome b genes of 116 individuals from six localities (between 05°44′S 80°53′W and 23°31′S 70°33′W). We found high levels of genetic diversity in the analyzed populations. No geographical structuring was observed in the haplotype network, which consisted of a few central, widely distributed haplotypes, and many derived population-specific haplotypes separated by few mutations. This pattern suggests a recent population expansion and moderate to low current gene flow among populations. Mismatch analysis, neutrality tests, and a Bayesian skyline analysis confirmed the occurrence of a past event of population expansion approximately 5,000 years ago, which coincides with increasingly stronger and more frequent El Niño events.