Our investigation of the phenylalanine/serine (Phe/Ser) protonated dimer suggests that the intermolecular interaction between the two amino acids is more complex than could have been anticipated from previous studies of similar systems. Isomer-specific infrared (IR) spectra, recorded at an internal temperature of ~10 K, demonstrate the presence of at least five isomers with nonzwitterionic structures. Moreover, isotopic substitution experiments provide evidence for different protonation sites among these isomers.