Ciguatoxin isolated from viscera of the moray eel Gymnothorax javanicus and its congener (tentative codename CTX-4B) isolated from the causative dinoflagellate Gambierdiscus toxicus were subjected to structure elucidation. The molecular formulae of C60H86O19 and C60H84O16 were determined for ciguatoxin and CTX-4B respectively, by HR-FABMS and 1H NMR measurements. 1H NMR signals of protons around a nine-membered ring were broadened or disappeared due to a slow conformational change of the ring, but spectra quality was improved by measuring at low temperature. By extensive use of 1H NMR 2D-correlation and NOE experiments carried out on 0.35 mg of ciguatoxin and 0.74 mg of CTX-4B, the two toxins were found to have brevetoxin-like polyether structures comprised of thirteen rings (7/6/6/7/7/9/7/6/8/6/7/6-spiro-5). CTX-4B was in a form less oxidized than ciguatoxin at two terminals of the molecule. Their relative stereochemistries, except for C2 of ciguatoxin, were clarified by detailed analyses of 1H NMR NOE experiments. The primary alcohol at the terminal of the ciguatoxin molecule suggested its usefulness for preparing a flourescent derivative or a toxin-protein conjugate to be used for immunization.