Many flowering plants exhibit self-incompatibility (SI) to prevent inbreeding and promote outcrossing. This self/non-self discrimination mechanism is controlled by the S locus, which contains separate genes for pistil and pollen specifcities. In the gametophytic SI (GSI) of Rosaceae, Solanaceae and Plantaginaceae, the pistil S determinant, S-RNase, encodes extracellular ribonuclease which is thought to act as a cytotoxin to the self pollen tube, while the pollen S determinant is the F-box gene called SLF/SFB/SFBB. In Petunia (Solanaceae), SLF is reported to be a component of the noncanonical E3 ubiquitin ligase complex with S-RNase binding protein1 (SBP1) and Cullin1 (CUL1), and interact with non-self S-RNases to ubiquitinate them for degradation. Here, we isolated an apple (Malus×domestica) homolog of SBP1 (MdSBP1) from pollen RNA by RT-PCR. MdSBP1 included a RING-HC domain required for E3 ubiquitin ligase activity, and showed 64.0-68.2% amino acid identities with solanaceous SBP1 proteins. Expression analysis showed that MdSBP1 was expressed in all the organs analyzed. We detected an interaction between recombinant MdSBP1 protein and S-RNase of apple using a pull-down assay. © 2013 The Japanese Society for Plant Cell and Molecular Biology.