Rim1 and Rim2 were originally described as specific Rab3A‐effector proteins involved in the regulation of secretory vesicle exocytosis. The putative Rab3A‐binding domain (RBD) of Rim consists of two α‐helical regions (named RBD1 and RBD2) separated by two zinc finger motifs. Although alternative splicing in the RBD1 of Rim is known to produce long and short forms of RBD (named Rim1 and Rim1Δ56‐105, and Rim2(+40A) and Rim2, respectively), with the long form of Rim1 and short form of Rim2 being dominant in mouse brain, the physiological significance of the alternative splicing in RBD1 has never been elucidated. In the present study I discovered that alternative splicing in Rim RBD1 alters Rab3A binding affinity to Rims, and found that insertion of 40 amino acids into the RBD1 of Rim2 (i.e. Rim2(+40A)) dramatically reduced its Rab3A binding activity (more than a 50‐fold decrease in affinity). Similarly, Rim1Δ56‐105 exhibited higher affinity binding to Rab3A than the long form of Rim1. Expression of the short forms of the Rim RBD in PC12 cells co‐localized well with endogenous Rab3A, whereas expression of the long forms of the Rim RBD in PC12 cells resulted in cytoplasimc and nuclear localization. Moreover, I found that Caenorhabditis elegans Rim/UNC‐10 (ce‐Rim) and Drosophila Rim (dm‐Rim) do not interact with ce‐Rab3 and dm‐Rab3, respectively, indicating that the Rab3‐effector function of Rim has not been retained during evolution. Based on these findings, I propose that the Rab3A‐effector function of Rim during secretory vesicle exocytosis is limited to the short form of the mammalian Rim RBD alone.