Two novel oligopeptide transporter cDNA clones, CPTA and CPTB, were identified by screening a Caenorhabditis elegans cDNA library using homology hybridization. The transporter proteins deduced from the cDNAs possess multiple transmembrane domains and reveal a moderate similarity to their mammalian counterparts in amino acid sequences. CPTA and CPTB, when expressed in Xenopus laevis oocytes and studied by both radiotracer flux and microelectrode voltage-clamp protocol, displayed a saturable electrogenic transport activity driven by a proton gradient with an overlapping broad spectrum of substrate specificity. Both transporters recognize di-, tri- and tetra-peptides including phenylalanylmethionylarginylphenylalaninamide (FMRFamide) and N-acetylaspartylglutamate, members of a large neuropeptide family commonly found throughout the animal kingdom. Kinetic analysis, however, revealed that CPTA and CPTB differed in their affinity for the peptide substrates, the former being a high-affinity type and the latter a low-affinity type. CPTA and CPTB are encoded by two distinct genes localized on separate chromosomes and are expressed during the whole life span of the organism.