Bacteria are continually exposed to foreign elements, such as bacteriophages and plasmids. It is very much archived that bacteria evolved defense systems against bacteriophages, which permit them to survive in an environment full of their predators. The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and CRISPR associated (Cas) genes adaptive immune systems provide heritable sequence-specific protection against these invaders. In this work the host Salmonella Enteritidis S49 was infected with its specific phage ΦSP-3 to isolate Bacteriophage Insensitive Mutants (BIMs). In order to understand the variation in the CRISPR regions of host and its mutants, they were amplified using specific primers of Salmonella. The amplicons obtained were sequenced and CRISPR identification was performed using CRISPRFinder online. Identities of CRISPR spacer regions were obtained using BLAST (Basic Local Alignment Search Tool). Host bacteria Salmonella Enteritidis S49 infected with its specific phage ΦSP-3 yielded BIMs. CRISPR regions were amplified and detected in CRISPRFinder online. A graphic representation of spacers based on its identity was prepared to analyse the spacer pattern in the BIMs and its host. Spacers were found deleted in certain BIMs and there was no novel addition of spacer in this case to infer CRISPR involvement in emergence of mutants. However, this study clearly shows that there were notable variations in spacer regions through phage challenges warranting further studies.