Recently, light-driven sodium pump rhodopsin (NaR/KR2/NDQ rhodopsin) and chloride pump rhodopsin (ClR/NTQ rhodopsin) from marine flavobacteria were identified by metagenomics study. One of them, light-driven sodium pump rhodopsin (NaR) structure was determined. The other one we have solved the first crystal structure of a unique class light-driven chloride pump (ClR) from Nonlabens marinus S1-08, at resolutions of 1.57 Å. Like structured Halorhodopsin (HR), ClR can transfer chloride ion from extracellular to cytosol. Although both ClR and HR are same light-driven chloride pump rhodopsin, we found some evidences that ClR and HR are different in structure and mechanism. In this structure, we suggest that how chloride ion transfer from extracellular to cytosol, determine significant residues for controlling functions and confirm light-driven pump activity through mutagenesis and functional assay. Also, unlike rhodopsin family, we found that ClR has structural differences such as ECL1 and Helix 8. These results suggest that together with NaR, ClR is a unique and new molecule for optogenetic study.