The discovery of functional cannabinoid receptor 2 (CB2R) in brain suggests a potential new therapeutic target for neurological and psychiatric disorders. However, recent findings in experimental animals appear controversial. Here we report that there are significant species differences in CB2R mRNA splicing and expression, protein sequences, and the receptor responses to CB2R ligands in mice and rats. Systemic administration of JWH133, a highly-selective CB2R agonist, significantly and dose-dependently inhibited intravenous cocaine self-administration under a fixed-ratio (FR) schedule of reinforcement in mice, but not in rats. However, under a progressive-ratio (PR) schedule of reinforcement, JWH133 significantly increased break-point for cocaine self-administration in rats, but decreased it in mice. To explore the possible reasons for these conflicting findings, we examined CB2R gene expression and receptor structure in the brain. We found novel rat-specific CB2C and CB2D mRNA isoforms in addition to CB2 A and CB2B mRNA isoforms of mice. In situ hybridization RNAscope assays found higher levels of CB2R mRNA in different brain regions and cell types in mice than in rats. By comparing CB2R-encoding regions, we observed a premature stop codon in the mouse CB2R gene, which truncated 13 amino acid residues including a functional autophosphorylation site in the intracellular C-terminus. These findings suggest that species differences in the splicing and expression of CB2R genes and receptor structures may in part explain the different effects of CB2R-selective ligands on cocaine self-administration in mice and rats.Neuropsychopharmacology accepted article preview online, 06 November 2014. doi:10.1038/npp.2014.297.