The structure of chlorophyllonic acid a methyl ester (3), a new chlorophyll a related compound was determined as shown in Fig. 2 by NMR spectral and X-ray crystallographic analysis. In the course of our screening for antioxidants from marine organisms we isolated new chlorophyll a related compounds, chlorophyllone a (1), chlorophyllonelactone a (2) and chlorophyllonic acid a methyl ester (3), as antioxidants in the dark from the short-necked clam. In this paper, we wish to describe the structure determination of 3. Compound 3 was obtained as a brown crystal, HR-FABMS m/z 563.2686 (MH⁺, +2.8 mmu for C₃₄H₃₅N₄O₄). By direct comparison of ¹H-NMR data of 3 with those of 2, 3 proved to have a chlorin ring system like 2 and a methoxy group (δ 4.04) in place of the hydroxy group (δ 5.86) of 2. The splitting pattern of H-7, -7a, -7a', -7b and -7b' of 2 and those of 3 are quite similar to each other. In the HMBC measurement of 3 long-range couplings from methoxy group (δ 4.04) to carbonyl carbon (δ 166.9) and from H-7b' to two other carbonyl carbon signals (δ 196.9, 192) were observed. These results postulated the structure of 3 with a methoxy carbonyl and 1,2-diketone group as shown in Fig. 1. There seems, however, to be very serious steric congestion between C-9 and C-10 carbonyls. The structure of 3 was confirmed by single crystal X-ray analysis, as shown in Fig. 2. The C-10 carbonyl of 3 is directed downward out of chlorin ring to reduce the steric congestion between the C-9 and C-10 carbonyls. Coupling constants of H-7a and H-7b and H-7a' and H-7b' in the ¹H-NMR of 3 in the solution exhibited eclipsed conformation of all these protons—the same conformation seen in the crystal structure. Compound 3 was confirmed to be present in the extracts of scallop and oyster, too. Compound 3 (3 µg) exhibited stronger antioxidative activity than α-tocopherol (20 µg) by a slightly modified thiocyanate method.