CRISPRs offer an alternative view on foreign DNA entering Legionella than the pan-genome estimated by comparative genomics. CRISPRs are bacterial adaptive immune systems for protection against DNA from non-hosts such as infecting phage33. They consist of cas genes and adjacent tandem arrays of short spacer DNA originating from the target organism. Cas-RNA spacer complexes destroy non-host DNA via specific binding. CRISPR spacer arrays are effectively a sampling of recently introduced foreign DNA. CRISPRs were previously identified in Lp Alcoy and Paris genomes15. Here, we identified another 22 ‘typical’ CRISPR sequences with at least two spacers in 13 Legionella genomes using CRISPRfinder34 (Supplementary Table 6). Some genomes had multiple CRISPR sequences: three were identified in Lp13 and Lp14, and two in Lp5, Lp7, and Lp11 (Supplementary Table 6; Supplementary Data 1). Lp5 had a CRISPR array with the highest number of spacers at 70. We also discovered questionable/putative CRISPRs that had one or few spacers (Supplementary Table 6; Supplementary Data 1). A CRISPR database search revealed the presence of four types of putative CRISPR-associated proteins: Cas large protein; Cas3; Cas1; and RAMP Csd1 family protein. Spacer sequences were specific for each strain. Of 555 spacer sequences in the Legionella genomes, 38 overlapped based on DNA sequence identity using the dnaclust tool35. Surprisingly, only 42/555 (7.6%) of the spacers were found to match a Legionella protein in the pan-genome database constructed using BLASTX with percent identity over the alignment length of >90%. Recently, Rao et al.36 identified 440 spacers in the L. pneumophila CRISPR-cas system, experimentally identifying the first known target of this system: a 30 kilobase episome (LME-1) of unknown function where interbacterial transfer is guarded against by CRISPR-Cas. Out of the 440 spacers identified, 277 spacers, of which 185 were unique, had exact matches with the 555 spacers identified in the present study. LME-1 was identified only in the Lp7 genome. These results suggest that a larger pool of foreign DNA infects Legionella than is reflected in the pan-genome, which counts only genes stably integrated into the genome.