In vitro cloning of Phalaenopsis hybrids is generally characterized by slow growth and low multiplication rates. Therefore, the impact of 6-(3-fluorobenzylamino)purine (FmT) and its 9-beta-D-riboside (FmTR) was evaluated. These halogenated compounds have been selected based on their very high cytokinin activity in previous bioassays. The Phalaenopsis plantlets formed significantly more, but smaller new shoots when treated with FmTR (25.3) compared to FmT (14.6) and BA (7.0). Furthermore, FmTR treatment completely abolished rooting during the micropropagation phase. Additionally, an interaction between cytokinin type and headspace aeration was noticed. For all treatments, the number of shoots increased significantly when grown in tightly closed containers. The use of fluorinated topolins might present a breakthrough in the in vitro micropropagation of Phalaenopsis.