Shrimp activity is associated with the impact of bacterial communities. Therefore, this research aimed to evaluate the influence of the bacterial microbiota on the organic matter content of the soil of the shrimp lagoon in La Segua- Ecuador. Starting from a descriptive approach, the field research method and documentary review were used. In total, 25 soil samples were collected in 5 quadrants of 100 m2. The bacterial DNA was extracted by using the Powersoil® kit and the identification of the strains was carried out with the 16SrDNA gene. The organic matter content was determined by Walkley-Black titration. The genus Bacillus was predominant in the bacterial strains; moreover, individuals of the genera Exiguobacterium, Acinetobacter, Prolinoborus, Arthrobacter Planococcus were identified with more than 99% homology for all cases. It was concluded that the organic matter content is suitable for shrimp farming.