A study was carried out to identify the microbial diversity in wastewater from the tuna industry, the samples were obtained at different points in the tuna process, the analysis was carried out using molecular tools such as metagenomics, the Electrophoresis technique in Denaturation Gradient Gel (DGGE) and Polymerase Chain Reaction (PCR). The sensitivity of these techniques allowed the amplification of 16S rDNA gene fragments by means of specific primers. This amplified PCR product was sent for sequencing, becoming a valuable alternative to provide information on the identity of the microbial population, characterizing the structure of an environment, obtaining 37 bacterial clones with 27.0% belonging to the Firmicutes group, 24.34% to Proteobacteria, 16, 21% to Actinobacteria.