Methylesterase family member 16 (MES16) is an integral component of chlorophyll breakdown. It catalyzes the demethylation of fluorescent chlorophyll catabolite (FCC) and pheophorbide in vitro, and specifically demethylates FCC in vivo. Here we report the crystal structure of MES16 from Arabidopsis thaliana at 2.8 Å resolution. The structure confirm that MES16 is a member of the α/β-hydrolase superfamily with Ser-87, His-239, and Asp-211 as the catalytic triad. Our biochemical studies reveal that MES16 has esterase activity with methyl-indole acetic acid as the substrate, and the catalytically essential role of Ser-87 has been demonstrated. •MES16 is a member of the α/β-hydrolase superfamily.•The cap domain of MES16 is differs from its homologues.•MES16 shows hydrolase activity to MeIAA.•Ser-87, His-239, Asp-211 are the catalytic triad and Ser-87 is essential for MES16' esterase activity.