Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs), together with cas genes, constitute the systems CRISPR-Cas, a novel type of innate defense system in prokaryotes for the destruction of exogenous elements (plasmids or phages). The genus Vibrio and Photobacterium represents one of the main responsible infectious agents in aquaculture and cause huge losses for the shrimp industry. The few bioinformatic investigations on CRISPR/Cas systems in the Vibrionaceae family are mainly oriented to clinical species. Therefore, the objective of this research was to make a comparative analysis of CRISPR-Cas systems in Vibrio and Photobacterium genomes of strong influence in aquaculture production. A total of 69 complete genomes across the family were studied. Seven CRISPR loci were identified in 4 species (V. parahaemolyticus, V. harveyi, V. vulnificus, and Photobacterium damselae). The CRISPR/Cas systems were found to correspond to subtypes I-E, I-F, and III-D. Only 47% of the spacers presented homology with bacteriophages. The results showed a low presence of CRISPR structures in the species of Vibrio and Photobacterium with immunity to specific phages. These results are interesting if sensitivity is considered, and it can be explored for the development of strategies such as phagotherapy in shrimp farming.