Phytochromes A and B have discrete photosensory functions in Arabidopsis. To determine whether differential temporal or spatial expression patterns of the PHYA and PHYB genes contribute to this phenomenon the expression of PHYA-GUS and PHYB-GUS reporter genes has been examined in transgenic Arabidopsis. Histochemical and quantitative biochemical analyses indicate that both transgenes are expressed extensively throughout the plant, including roots, shoots and flowers, during the entire life cycle, but with strong differences between the two in expression level and photoregulation, and more limited differences in spatial expression patterns. The data indicate that regulation is at the transcriptional level. In dry seed, PHYB-GUS is expressed throughout the embryo at three-fold higher levels than PHYB-GUS, which is confined primarily to the embryonic root tip. By contrast, PHYA promoter activity, despite strong negative regulation in shoots by light, is consistently higher than PHYB (two- to 20-fold) in both the light and dark in most tissues during all subsequent developmental phases, from seedling to mature adult. At the tissue level, most cells appear to express both transgenes at some level at all stages examined, with highest apparent activity in vascular tissue and root tips. With the notable exception of pollen, where high PHYB-GUS but not PHYA-GUS expression occurs, few major differences are observed in the quantitative spatial distribution pattern between the two transgenes. The strongly similar spatial and temporal expression patterns of PHYA-GUS and PHYB-GUS transgenes suggest that the differential photosensory activity of these two phytochromes occurs largely through differences in their (i) intrinsic biochemical activities, (ii) relative abundances, and/or (iii) independent and separate reaction partners, rather than through discrete, developmentally controlled expression patterns.