In order to demonstrate the potential of plant cell culture systems to produce a target natural bioactive compound, we proposed a stepwise protocol for β-thujaplicin production as follows. 1. Induction phase: Characteristics of callus cultures originating from newly flushed shoots of 10 conifer species were evaluated on different basal media such as Murashige and Skoog (MS), Schenk and Hildebrandt (SH), and Lloyd and McCown's Woody Plant medium (WP) containing 10 μM 2,4-dichlorophenoxyacetic acid (2,4-D) either alone or in combination with 1 μM of N6-benzyladenine (BA). The conifer species used were as follows: Chamaecyparis (C. obtusa Sieb. et Zucc. and C. pisifera Sieb. et Zucc.), Juniperus (J. chinensis L. 'Kaizuka', J. chinensis L. var. sargentii, and J. conferta Parlatore), Thuja (T. occidentalis L. and T. standishii (Gord.) Carr.), Thujopsis (T. dolabrata Sieb. et Zucc. and T. dolabrata Sieb. et Zucc. var. hondae), and Cryptomeria (C. japonica D. Don). We observed the phenotypes of each callus to determine the optimal conditions for callus induction and to infer biosynthetic activity of the calli over 4-8 weeks. 2. Habituation phase: Each of the cell cultures obtained was transferred to a modified MS medium containing 680 mg L(-1) KH2PO4 and 10 μM Picloram to select the habituated cells with synchronous growth pattern. The growth of each cell culture was highly improved in the habituation medium, except that of J. chinensis 'Kaizuka'. 3. Metabolite-production phase: The concentration of β-thujaplicin (known as hinokitiol in Japan) in the shoots of donor trees and the habituated cell cultures was analyzed via high-performance liquid chromatography (HPLC). Histochemical characteristics of the cells were also observed using laser scanning microscopy (LSM) imaging. After the third step, we tested the biosynthetic activity of two habituated calli (C. obtusa and J. conferta) on a 0.3%, w/v, yeast extract (YE)-containing medium. We found significant improvement in β-thujaplicin production in J. conferta callus (4600 μg g DW-1), which was up to 20-fold higher than in the habituation phase.