The Peruvian scallop (Argopecten purpuratus, Lamarck 1989) is a marine bivalve of high commercial value in the aquaculture industry, with wild populations distributing from northern Peru to Chile. Its growing demand in the world aquaculture markets and limited availability of hatchery-based seeds, caused long-term seed translocations among wild populations to recover depleted local populations and for production needs. We investigated long-term translocations effects on the genetic diversity and structure of wild populations using next-generation RAD sequencing. We sampled individuals from Sechura, Lobos de Tierra, Samanco and Bahia Independencia in Peru, and La Rinconada in Northern Chile. We identified 6275 polymorphic RAD tags and 8345 SNPs for the five populations. We estimated high observed heterozygosity for all populations and high SNP frequency compared to similar studies on marine bivalves. We detected no spatial divergence among populations in Peru (pairwise FST ranged from 0 to 0.003), but strong differentiation with the population in Chile. Migration rate estimates suggested asymmetric directionality of seed translocation. Overall, our results support a remnant effect of an intense historic translocation and on-going gene flow among wild populations in Peru, challenging the identification of outlier loci and certification of sustainable origin of cultured scallops using genetic markers.