The overall processes of transcription and its regulation have advanced significantly in the last years, making our understanding of prokaryotic biology more complex and detailed. In fact, a systematic study of different aspects of transcriptional regulation opens up outstanding opportunities to improve and develop the perception of complex reaction mechanisms, genetic processes and cell functions. In close connection to the cyanobacterial bidirectional hydrogenase, the main hydrogen-evolving enzyme in non-nitrogen fixing strains, two novel transcription factors have received increasing attention over the past five years: a LexA-related protein and the AbrB-like family members. Recent work on these regulators has produced new insights and advances towards the understanding (and possible interconnection) of several regulatory networks in cyanobacteria, namely nitrogen metabolism, redox response, toxin production, CO2 concentrating mechanisms and hydrogen metabolism. The fact that a LexA-related protein and AbrB-like family members have been co-purified in independent laboratories studying different sets of cyanobacterial genes suggests a possible common and/or complementary function of these regulators. In this review, we summarize the knowledge gained thus far regarding the transcriptional regulation of the cyanobacterial bidirectional hydrogenase, with special focus on the above mentioned transcription factors. Moreover, we discuss several additional points that warrants further investigation to increase our knowledge in this fast evolving research field.