Although evidence for LexA-orthologues, which do not regulate DNA damage repair, is accumulating, identification of binding sites and regulon members remains poorly characterized. In the cyanobacterium, Synechocystis sp. strain PCC 6803, we have recently identified a LexA-related protein that regulates expression of the crhR RNA helicase gene. Here we show that the Synechocystis LexA-orthologue binds as a dimer to 12 bp direct repeats containing a CTA-N9-CTA sequence conserved in two target genes, lexA and crhR. Characterization of this site provides the basis for identification of additional LexA targets and further evidence for LexA's divergence during evolution.