We have developed a simple and effective molecular imprinting technique to target compounds with flexible structure. Domoic acid (DA), an amnesic shellfish poison, was used as the target compound while many acidic compounds (mono-, di-, and tricarboxylic acids) were used as template molecules for molecularly imprinted polymers (MIPs). Evaluation of selective recognition abilities using liquid chromatography revealed that the highest selective recognition ability for DA was found when pentane-1,3,5-tricarboxylic acid (1,3,5-PeTA) was used as the template. Computer modeling studies of the DA structure suggested that the observed selective recognition depended on the structural changes in DA at the recognition site of the MIPs as well as spatial distance between the COOH groups in DA and 1,3,5-PeTA. Using the 1,3,5-PeTA-MIP, we could easily purify DA from blue mussel extracts by solid-phase extraction.