The northern mangrove coast of Brazil comprises the Brazilian states of Amapá, Pará and Maranhão. Fishes from the coastal mangrove region form a principal component of the local fishery, and account for 58% of all fish landed. The most commonly landed fishes are those of the family Sciaenidae. Cynoscion acoupa is one of the most exploited sciaenid species, with over 600 tons landed each year. Therefore, we developed 17 microsatellite markers to investigate genetic variability and population structuring of this species along the coast of Brazil.