A novel compound, purpurone (1), with ATP-citrate lyase (ACL) inhibitory activity, was isolated from the marine sponge Iotrochota sp. Given the key role of low-density lipoproteins (LDL) in hypercholesterolemia, agents that stimulate LDL catabolism or inhibit its synthesis are of significant interest for disease treatment. As very-low-density lipoproteins (VLDL), the metabolic precursors of LDL, are produced from fatty acids and cholesterol, intervening in VLDL synthesis at the acetyl CoA and citrate lyase level represents a strategic therapeutic target. While HMG-CoA reductase inhibitors reduce cholesterogenesis by interfering with the conversion of acetyl CoA to mevalonic acid, ACL inhibitors are anticipated to decrease acetyl CoA production, thereby affecting both lipogenesis and cholesterogenesis. During the screening of natural products for ACL activity, an extract of Iotrochota sp. was selected. The aqueous ethanol extract of Iotrochota sp. (from Suntory) exhibited good ACL inhibitory activity with an IC50 of 25 μg/mL. Purpurone was isolated via mild acid hydrolysis (2 N methanolic HCl) followed by repeated RP18 HPLC purification. Purpurone is a purple, noncrystalline glassy solid with a molecular formula of C40H28NO11 (established by HRFABMS, [M + H]+ m/z = 698.1673). Structural elucidation revealed a highly symmetrical molecule, supported by NMR (22 carbon signals, 9 proton signals), IR (hydroxyl and carbonyl bands), UV (phenolic group characteristics), and permethylation studies (indicating nine phenolic groups). Biologically, purpurone inhibits ACL in a dose-dependent manner with an IC50 of 7 μM. It shows no cytotoxicity to Hep G2 cells, with no reduction in cellular ATP levels at 100 μg/mL. Preliminary data suggest it reduces fatty acid biosynthesis but does not affect cholesterol biosynthesis.