Free fatty acid profiles of wild type and fatty acyl-ACP synthase deletion mutant strain of Synechocystis sp. PCC6803 indicated that one origin of these fatty acids is the process of lipid remodeling or lipid degradation. Lipase is the key enzyme involved in this process. The gene sll1969 is the sole gene encodes a putative lipase in Synechocystis sp. PCC6803. To identify the function of this gene and its role in fatty acid metabolism, we cloned the sll1969 from genomic DNA, overexpressed it in Escherichia coli BL21 (DE3) using pET expression system and purified this recombinant enzyme with Nickel-nitrilotriacetic acid affinity chromatography. The enzyme activity was assayed by spectrophotometric with p-nitro-phenylbutyrate as substrate. The Km and kcat of the enzyme is (1.16±0.01) mmol/L and (332.8±10.0)/min, respectively toward p-nitro-phenylbutyrate at 30 oC. The optimal temperature of the enzyme is 55 oC. To investigate the biological role of Sll1969 in fatty acid metabolism in cyanobacteria, we constructed sll1969 deletion and overexpression mutant strains in the background of fatty acyl-ACP synthase deletion mutant of Synechocystis sp. PCC6803. The analyses of the content of free fatty acids in different mutant strains showed that the contents of Sll1969 and free fatty acid are positively correlated. The free fatty acid profiles of the sll1969 mutant strains suggested this enzyme is not the sole enzyme for degrading lipid in Synechocystis sp. PCC6803.