Ciguatoxins are the major causative toxins in ciguatera seafood poisoning. The limited availability of ciguatoxins has precluded structural elucidation and development of a reliable and specific immunoassay for detecting the toxins in contaminated fish. To seek a solution for the longstanding problem of ciguatera, we addressed the synthetic challenge by utilizing rationally designed model compounds of ciguatoxins. The C2 configuration and entire absolute configuration of ciguatoxin were successfully elucidated with minutest amounts of natural toxins, using an approach which combined partial structure synthesis, microscale chemical transformations, and the CD exciton chirality method. On the basis of the absolute configuration, the partial structures of ciguatoxins were designed and synthesized as haptens for the preparation of anti-ciguatoxin antibodies. Monoclonal antibodies (mAbs) against both ends of ciguatoxin CTX3C were prepared by immunization of mice with protein conjugates of synthetic haptens of the ABCDE-ring and the IJKLM-ring, in place of the natural toxin. Haptenic groups with surface areas larger than 400 Å 2 were required to produce mAbs, which could bind strongly to CTX3C itself. A direct sandwich enzyme-linked immunosorbent assay (ELISA) using these mAbs was shown to detect CTX3C at the ppb level with no cross-reactivity against other related marine toxins, including brevetoxin A, brevetoxin B, okadaic acid, or maitotoxin. In order to make the sandwich immunoassay protocol a general method for detecting other ciguatoxins congeners, the preparation of mAbs for the left-end of ciguatoxin was investigated. Expeditious synthesis of the left end of ciguatoxin with installation of the 3-butene-1,2-diol side-chain of the A-ring as well as surface plasmon resonance (SPR) analysis of the antibody-hapten interactions are also described.