Plants fine-tune light responses through interactions between photoreceptors. We have previously reported that the greening of Arabidopsis thaliana roots is regulated synergistically by phytochromes and cryptochromes. In the present study, we investigated the functions of the N- and C-terminal domains of phytochrome B (phyB) in the interactions between phyB and cryptochrome signaling cascades. Transgenic Arabidopsis expressing the phyB N-terminal domain fused to green fluorescent protein (GFP), beta-glucuronidase (GUS) and the nuclear localization signal (NLS) showed intense root greening under blue light, indicating that the C-terminal domain was dispensable for the synergistic interaction in the induction of root greening. However, root greening under red light was substantially reduced in the absence of the C-terminal domain. This effect was opposite to the previous observation that removal of the C-terminal domain enhanced the signaling activity of phyB in the inhibition of hypocotyl elongation. In addition, we found that overexpression of the isolated C-terminal domain of phyB enhanced the blue light response not only for root greening but also for the inhibition of hypocotyl elongation. Analysis of this activity on various photoreceptor mutant backgrounds demonstrated that the isolated C-terminal domain enhanced cryptochrome signaling. In summary, these results demonstrate that different domains of phyB can play various roles which are dependent on light conditions as well as on the specific physiological response.