Inter-subgeneric hybrids were successfully obtained in reciprocal cross combinations between evergreen azaleas (Rhododendron nakaharae and its hybrids) and fragrant deciduous azaleas (R. arborescens and R. viscosum) for the purpose of fragrant evergreen azalea breeding. Nuclear and organelle DNA of these hybrids was investigated using PCR-RFLP markers. Viable hybrid seedlings have nuclear ribosomal DNA (nrDNA) inherited biparentally, mitochondrial DNA (mtDNA) from the seed parent, and chloroplast DNA (cpDNA) from the deciduous azalea, regardless of cross combination. These results suggest that the chloroplast genome from deciduous azaleas and the nuclear genome from evergreen azaleas are compatible in viable hybrid progenies.