We clarified the appearance of albino seedlings caused by plastome-genome incompatibility in intersectional hybridisation between evergreen azaleas and deciduous Rhododendron japonicum f. flavum. Intra- and inter-ploid crosses of 2x and 4x evergreen azaleas x 2x R. japonicum f. flavum, respectively, showed high capsule set, but their reversed crosses resulted no capsule set. Green and albino hybrids were obtained from 2x evergreen azaleas x 2x R. japonicum f. flavum where ptDNAs of the green and albino plants were derived from R. japonicum f. flavum (paternal parent) and evergreen azaleas (maternal parents), respectively. All the progenies in the crosses of 4x evergreen azaleas x 2x R. japonicum f. flavum were green triploids with evergreen azalea-derived ptDNA. The efficiency of obtaining green hybrids in inter-ploid crosses was higher than that in intra-ploid crosses. These results suggest that inter-ploid crosses of 4x evergreen azaleas x 2x R. japonicum f. flavum can overcome plastome-genome incompatibility between evergreen azalea-derived plastome and hybrid nuclear genome.