Clustered, regularly interspaced short palindromic repeats (CRISPR) and the Cas-associated proteins (Cas) system (CRISPR-Cas) have been studied as a bacterial immune system that functions by preventing the entry of mobile genetic elements via nucleases. It has been demonstrated by bioinformatics analysis that the CRISPR-Cas system is distributed among some species of the genus Aeromonas, predominantly type I, specifically subtypes I-F and I-E, and to a lesser extent type I-C. Aeromonas caviae and A. veronii are the species with the highest prevalence rate of these systems, about 20–22%, and the presence of the type I-E, I-F, I-C, III-D systems has also been demonstrated in genomes of Mexican isolates. By understanding the activity of Cas proteins, some methodologies have been developed for the detection of pathogens such as viruses and bacteria. Aeromonas has been applied to detect virulent strains in food samples, blood cultures, and feces, as well as to detect genes encoding for antibiotic resistance in other genera.