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Increasing evidence has shown that light exists in a diverse range of deep‐sea environments. We unexpectedly found that blue light is necessary to produce excess zero‐valent sulfur (ZVS) in Erythrobacter flavus 21‐3, a bacterium that has been recently isolated from a deep‐sea cold seep. E. flavus 21‐3 is able to convert thiosulfate to ZVS using a novel thiosulfate oxidation pathway comprising a thiosulfate dehydrogenase (TsdA) and a thiosulfohydrolase (SoxB). Using proteomic, bacterial two‐hybrid and heterologous expression assays, we found that the light–oxygen–voltage histidine kinase LOV‐1477 responds to blue light and activates the diguanylate cyclase DGC‐2902 to produce c‐di‐GMP. Subsequently, the PilZ domain‐containing protein mPilZ‐1753 binds to c‐di‐GMP and activates TsdA through direct interaction. Finally, Raman spectroscopy and gene knockout results verified that TsdA and two SoxB homologs cooperate to regulate ZVS production. As ZVS is an energy source for E. flavus 21‐3, we propose that deep‐sea blue light provides E. flavus 21‐3 with a selective advantage in the cold seep, suggesting a previously unappreciated relationship between light‐sensing pathways and sulfur metabolism in a deep‐sea microorganism. Synopsis: Blue light has been shown to affect metabolism in certain deep‐sea bacteria. Here, we show that blue light promotes the formation of zero‐valent sulfur (ZVS) in the deep‐sea cold‐seep bacterium Erythrobacter flavus 21‐3 via a pathway involving a light‐sensing LOV histidine kinase and downstream c‐di‐GMP production. Blue light stimulates the production of zero‐valent sulfur (ZVS) in E. flavus 21‐3.The light–oxygen–voltage histidine kinase LOV‐1477 phosphorylates the diguanylate cyclase DGC‐2902 and promotes the production of c‐di‐GMP.mPilZ‐1753 binds c‐di‐GMP, activating thiosulfate dehydrogenase (TsdA) via a direct interaction.Two thiosulfohydrolase (SoxB) homologs collaborate with TsdA to generate ZVS. [ABSTRACT FROM AUTHOR]