Arsenate reductases are the key enzymes in biological arsenic detoxification by catalyzing the intracellular reduction of arsenate to arsenite, and arsenite could be subsequently pumped out of the cells by ArsB or Acr3. The arsenate reductase from cyanobacterium Synechocystis sp. Strain PCC 6803 (SynArsC) shows sequence homology with the thioredoxin-dependent arsenate reductase family, while utilizes the glutathione/glutaredoxin system for arsenate reduction. SynArsC is classified as a novel thioredoxin/glutaredoxin hybrid arsenate reductase family. Here we report the crystal structures of SynArsC in the native and phosphate-bound states at 1.37 and 1.55 Å resolutions, respectively. The structures are mostly similar, but also show differences with implications in SynArsC’s arsenate reduction mechanism. Our results provide insights into SynArsC’s structure-function relationship and its enzymatic mechanism.