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Background  Bacteria are prey for many viruses that hijack the bacterial cell in order to propagate, which can result in bacterial cell lysis and death. Bacteria have developed diverse strategies to counteract virus predation, one of which is the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated (Cas) proteins immune defense system. Species within the bacterial family  Vibrionaceae  are marine organisms that encounter large numbers of phages. Our goal was to determine the significance of CRISPR-Cas systems as a mechanism of defense in this group by investigating their prevalence, phylogenetic distribution, and genome context.    Results  Herein, we describe all the CRISPR-Cas system types and their distribution within the family  Vibrionaceae . In  Vibrio cholerae  genomes, we identified multiple variant type I-F systems, which were also present in 41 additional species. In a large number of  Vibrio  species, we identified a mini type I-F system comprised of  tniQcas5cas7cas6f , which was always associated with Tn7-like transposons. The Tn7-like elements, in addition to the CRISPR-Cas system, also contained additional cargo genes such as restriction modification systems and type three secretion systems. A putative hybrid CRISPR-Cas system was identified containing type III-B genes followed by a type I-F  cas6f  and a type I-F CRISPR that was associated with a prophage in  V. cholerae  and  V. metoecus  strains. Our analysis identified CRISPR-Cas types I-C, I-E, I-F, II-B, III-A, III-B, III-D, and the rare type IV systems as well as  cas  loci architectural variants among 70 species. All systems described contained a CRISPR array that ranged in size from 3 to 179 spacers. The systems identified were present predominantly within mobile genetic elements (MGEs) such as genomic islands, plasmids, and transposon-like elements. Phylogenetic analysis of Cas proteins indicated that the CRISPR-Cas systems were acquired by horizontal gene transfer.    Conclusions  Our data show that CRISPR-Cas systems are phylogenetically widespread but sporadic in occurrence, actively evolving, and present on MGEs within  Vibrionaceae .    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5439-1) contains supplementary material, which is available to authorized users.

CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species