The pink shrimp Penaeus notialis is one of the most important commercial species of the world. In the Caribbean Sea of Colombia, they represent 70 % of the catches in industrial fisheries, but since the 90’s it has shown a significant decrease in its abundances because of overexploitation of the resource. Because there are no studies on the genetic status of their populations in the Colombian Caribbean, the current management strategies for the pink shrimp can be improved with genetic criteria. Hence, the objective of this study was to examine the genetic diversity (Ho, He and Fis), structure population (Fst, AMOVA, Bayesian analysis, DAPC, Mantel test) and the connectivity (assignment analysis) in five localities distributed in the Caribbean Sea of Colombia (Zapatá, Arbolete, Isla Fuerte, Punta Canoa y Manaure). Additionally, we assessed the spatial distribution of size structure by geostatistical analysis to identify possible nursery areas and a relationship with the genetic structure observed. The genetic analyses using seven microsatellites loci, showed low genetic diversity (Ho < 0,35), high genetic potential (He < 0,93), high inbreeding (Fis> 0,6) and the presence of three populations (ФST2, 98 = 0,065; P < 0.001) showing significant adjustment to the isolation-by-distance model (r = 0,78, z = −27,92; p = 0,031). It is discussed how the life cycle of the species, geomorphological variations on the continental shelf and marine currents influence the spatial distribution of size structure and genetic lineages of the pink shrimp, as well as the implications of this type of studies in the sustainable management of this valuable fishing resource.