We aimed to produce intergeneric hybrid plants with only one or a few alien chromosomes via microprotoplast fusion for genetic improvement and chromosome studies in Liliaceous ornamental plants. In order to apply this technique, it is essential to establish an efficient system for mass-preparation of microprotoplasts. We have established 2 different systems for isolating microprotoplasts, one from partially synchronized cell suspension cultures of Hemerocallis hybrida and the other from developing microspores of Lilium longiflorum. Here, the induction of micronucleated cells, isolation of microprotoplasts, and enrichment of smaller microprotoplasts containing one or a few chromosomes are described for both systems.