<jats:title>Abstract</jats:title><jats:p>Regulatory sRNAs in photosynthetic cyanobacteria have been reported, but the lack of plausible RNA chaperones involved in this regulation appears enigmatic. Here, we analyzed the full ensemble of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) in<jats:italic>Synechocystis</jats:italic>6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished supporting a high quality of the approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include a YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma-antisigma complexes is suggested. The<jats:italic>Synechocystis</jats:italic>Grad-seq resource is available online at<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/">https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/</jats:ext-link>, providing a comprehensive resource for the functional assignment of RNA-protein complexes and multisubunit protein complexes in a photosynthetic organism.</jats:p><jats:sec><jats:title>One-sentence summary</jats:title><jats:p>We provide the first global analysis of a cyanobacterium using Grad-seq, providing a comprehensive resource for the in-depth analysis of the complexome in a photosynthetic organism.</jats:p></jats:sec>