Neonicotinoid agonists selectively act on the insect nicotinic acetylcholine receptor (nAChR). The molecular basis for this specificity is deciphered by comparisons of two acetylcholine binding proteins (AChBPs) with distinct pharmacological profiles that serve as structural homologues for the nAChR subtypes. Aplysia AChBP has high neonicotinoid sensitivity, whereas Lymnaea AChBP has low neonicotinoid sensitivity, pharmacologies reminiscent of insect and vertebrate nAChR subtypes, respectively. The ligand-receptor interactions for these AChBPs were established by chemical and structural neurobiology approaches. Neonicotinoids and nicotinoids bind in a single conformation with Aplysia AChBP, wherein the electronegative nitro or cyano pharmacophore of the neonicotinoid faces in a reversed orientation relative to the cationic nicotinoid functionality. For Lymnaea AChBP, the neonicotinoids have two binding conformations in this vertebrate receptor model, which are completely inverted relative to each other, whereas nicotinoids are nestled in only one conserved conformation. Therefore, the unique binding conformations of nicotinic agonists determine the selective receptor interactions.