FtsH proteases are found throughout nature and contain a conserved ATPase domain, flanked by an N-terminal transmembrane domain and a Zn2+-binding protease domain. They play diverse roles in maintaining cellular activity. In the case of oxygenic photosynthetic organisms, FtsH-mediated degradation of damaged D1 protein is crucial for the operation of the photosystem II repair cycle needed to prevent photoinhibition. Four FtsH homologues are present in the model cyanobacterium Synechocystis sp. PCC 6803. One of these, FtsH2 (Slr0228), is known to be important for D1 degradation. However the structure of the FtsH2 complex is unknown and little is known about the structure and function of the other FtsH homologues. In this work, all four FtsH homologues were isolated via C-terminal GST tagging in tandem with affinity chromatography. Analysis of the purified FtsH complexes revealed the presence of FtsH1(Slr1390)/FtsH3(Slr1604) and FtsH2/FtsH3 heterocomplexes, whereas FtsH4 (Sll1463) appeared to form homocomplexes. Single particle analysis using electron microscopy revealed that the FtsH2-GST/FtsH3 complex was a hexameric particle of diameter ~120 Å with the two types of protomer alternately arranged around the central pore. Inactivation of the protease activity of FtsH2 did not abolish the function of the FtsH2/FtsH3 complex. FtsH2 and FtsH4 are mainly localised in the thylakoid membranes, whereas FtsH3 is dual targeted to both thylakoid and cytoplasmic membranes. FtsH1 is likely to be present in the cytoplasmic membrane. In vitro studies of E. coli over-expressed cytosolic domains of FtsH from Thermosynechococcus elongatus confirmed that the FtsH2, FtsH3 and FtsH4 homologues exhibited both ATPase and CTPase activity but that only FtsH4 could degrade casein. Homologues of E.coli YccA (Sll1150) and Arabidopsis EGY2 (Sll0862) were co-purified with the FtsH2-GST/FtsH3 complex. However, preliminary studies suggest neither is critical for FtsH-mediated D1 degradation. Strikingly, Psb29 (Sll1414) was found to be important for accumulation of FtsH2/FtsH3 complex, but further work is required to determine the mechanism.