The presence of small RNAs (sRNA) and their functions in transcriptional regulation has lately turned into a hot topic. Since cyanobacteria often face changes in the surrounding environment, they need to have a well working system for stress response. Quick adaption is necessary, and an RNA-based regulatory system is thus useful. One example of these sRNAs is CRISPRs. In this work we report the existence of a CRISPR within the hyp-operon (hyp genes encode proteins responsible for the maturation of hydrogenases) of the filamentous cyanobacterium Nostoc sp. strain PCC 7120. We present data concerning its characteristics and putative function(s) and raise the question concerning the importance of this CRISPR array and other CRISPR systems in general. In addition, we discuss the use of the CRISPR system as a potential bacterial genetic defence mechanism to achieve robust, cyanobacterial cultures in large scale, commercial production units. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.