Scopolia parviflora Nakai, a rare and endangered species, is the sole plant producing tropane alkaloids (TA) among the Korean native species. In order to enhance TA productivity the SP72 root line was selected by screening 100 of root line, and the optimal culture media for root growth and TA production were investigated with the SP72 roots. Based on the several media, SH and 2B5 medium were determined as growth medium and White and NN medium as production medium. Among the four combinations of two-stage culture, 2BN (2B5 as growth medium plus NN as production medium) showed more enhanced root growth and TA production as compared with production media of White and NN medium and growth media of SH and 2B5 medium, respectively. However, bubble column bioreactor (BCB) cultures applying two-stage culture did not reveal the effective results despite of the each successful operation of two-stage culture in conical flasks and BCB cultures.