CRISPRFinder is a web-based tool designed to identify clustered regularly interspaced short palindromic repeats (CRISPRs) in prokaryotic genomes. CRISPRs are tandem repeats found in many bacteria and archaea, consisting of direct repeats (DRs) separated by unique spacer sequences. The tool allows detection of CRISPRs, including the shortest ones, defines DRs and spacers, identifies flanking sequences to determine the leader, blasts spacers against GenBank, and checks if DRs are present elsewhere in prokaryotic genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php. The tool uses a four-step process: (1) identifying maximal repeats, (2) selecting the DR consensus based on occurrence and score, (3) defining candidate CRISPRs, and (4) eliminating tandem repeats. It provides a detailed output, including the number of confirmed and questionable CRISPRs, visual representation of DRs and spacers, and links to summary files and BLAST results. Users can also analyze CRISPR loci by blasting spacers against databases, viewing flanking sequences, and identifying identical DRs in other CRISPR loci. CRISPRFinder offers several advantages over existing tools, including the ability to detect short CRISPR-like structures, accurate DR definition, and easy extraction and blasting of flanking sequences or spacers. It is user-friendly and accessible online, making it a valuable resource for CRISPR research. The tool has been validated against other studies and has successfully identified CRISPRs in various organisms, including those previously thought to lack them. CRISPRFinder is an essential tool for CRISPR analysis, providing accurate and efficient identification of CRISPRs in genomic sequences.CRISPRFinder is a web-based tool designed to identify clustered regularly interspaced short palindromic repeats (CRISPRs) in prokaryotic genomes. CRISPRs are tandem repeats found in many bacteria and archaea, consisting of direct repeats (DRs) separated by unique spacer sequences. The tool allows detection of CRISPRs, including the shortest ones, defines DRs and spacers, identifies flanking sequences to determine the leader, blasts spacers against GenBank, and checks if DRs are present elsewhere in prokaryotic genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php. The tool uses a four-step process: (1) identifying maximal repeats, (2) selecting the DR consensus based on occurrence and score, (3) defining candidate CRISPRs, and (4) eliminating tandem repeats. It provides a detailed output, including the number of confirmed and questionable CRISPRs, visual representation of DRs and spacers, and links to summary files and BLAST results. Users can also analyze CRISPR loci by blasting spacers against databases, viewing flanking sequences, and identifying identical DRs in other CRISPR loci. CRISPRFinder offers several advantages over existing tools, including the ability to detect short CRISPR-like structures, accurate DR definition, and easy extraction and blasting of flanking sequences or spacers. It is user-friendly and accessible online, making it a valuable resource for CRISPR research. The tool has been validated against other studies and has successfully identified CRISPRs in various organisms, including those previously thought to lack them. CRISPRFinder is an essential tool for CRISPR analysis, providing accurate and efficient identification of CRISPRs in genomic sequences.