In vitro bulb scales of Lilium longiflorum×L. formosanum were used as explants to develop a highly efficient regeneration system. A high regeneration rate (100%) was reached through organogenesis on basal Murashige and Skoog (MS) medium supplemented with 1.0 mg/l 6-benzylaminopurine (6-BA) and 1.0 mg/l naphthaleneacetic acid (NAA). A genetic transformation system for the lily was developed using an Agrobacterium tumefaciens-mediated method. An improved genetic transformation rate (12‰) was obtained when the explants were pre-cultured for 3 days, immersed in bacterial suspension (OD600≈0.8) for 5 min, and co-cultivated for 5 days. The binary vector pBI121 containing Zm401, a maize pollen-specific gene, was introduced into the Agrobacterium strain LBA4404 and transformed into the explants using the genetic transformation system. Gene integration into the lily genome was confirmed by polymerase chain reaction (PCR) and PCR–Southern analysis. These results could lead to the production of new pollenless lily plants.