CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) systems constitute prokaryotic adaptive immune mechanisms that provide targeted protection against invasive genetic elements, including bacteriophages and plasmids (Barrangou et al., 2007). In the oral cavity, where dense polymicrobial communities engage in continuous viral-host interactions and horizontal gene transfer, CRISPR-Cas locus architectures record historical viral exposures and evolutionary dynamics. To support the exploration of microbial defense networks across oral taxa, eHOMD integrates an automated CRISPR-Cas detection engine that dynamically maps CRISPR repeat-spacer arrays and associated Cas gene clusters across all reference genomes. This analytical capability allows researchers to investigate host-phage co-evolution, profile adaptive immune repertoires, and track functional genomic variability across oral and aerodigestive microflora. The current result of the CRISPR-Cas system detection was done with CCTyper (version 1.8.0) - an automatic detection and subtyping of CRISPR-Cas operons with the default parameter (Russel et al., 2020). A total of 4,165 out of the 8,177 genomes annotated in HOMD were detected to possess the CRISPR-Cas system. The results are tabulated into a table listing the genomes with detected CRISPR-Cas system and links to the Genome Viewer and the original data output by CCTyper are also provided below.