Southern white shrimp Litopenaeus schmitti has been a commercial exploited species in Colombian Caribbean since 1968, becoming a high trade interest species and carrying a development of high fiheries activity, which then caused an overexploitation and a subsequent decrease in catches. Due to the current situation of this species, with the aim of assess the genetic diversity and the level of differentiation within each population and between different populations of the southern white shrimp with help of microsatellite molecular markers, 162 individuals were fihed from four shore locations; Laguna de Navío Quebrado in La Guajira, Ciénaga Grande de Santa Marta in Magdalena, Bahía de Barbacoas in Bolívar and Bahía de Cispatá in Sucre; and one open sea population in Golfo de Morrosquillo, Córdoba and Sucre shores. It was found that Navío Quebrado’s population showed the highest level of observed heterocigosity and Ciénaga Grande's population showed the lower level of inbreeding. According to the analysis of population structure, there are three population units; one consisting of Ciénaga Grande, Bahía de Barbacoas, and Cispatá populations, another consisting of Golfo de Morrosquillo population, and a third one consisting of Laguna de Navío Quebrado; these fidings could be results of the oceanographic current patterns.