Previously, two pools of phytochrome A (phyA′ and phyA″) have been detected by in situ low-temperature fluorescence spectroscopy and photochemistry; it was suggested that they might differ in the nature of their posttranslational modification. In order to verify this possibility Arabidopsis and rice (Oryza) phyA were expressed in yeast and the pigments were assembled in vivo with phycocyanobilin (PCB) and phytochromobilin (PΦB). The resulting recombinant phytochromes in the red-light–absorbing form (Pr) were characterized in the yeast cell by (1) the fluorescence emission spectra; (2) the temperature dependence of Pr fluorescence intensity and activation energy of fluorescence decay; and (3) the extent of photoconversion of Pr into photoproduct lumi-R (γ₁) or far-red–light absorbing form (Pfr) (γ₂). Both Arabidopsis phyA/PCB and Oryza phyA/PΦB had low γ₁ of ca 0.05, allowing their attribution to the Pr″ phenomenological type of phytochrome comprising phyA″, phyB and cryptogam phytochromes. The spectroscopic properties of Oryza phyA/PΦB were also very close to phyA″. However, both investigated holoproteins differed from phyA″, both with respect to the character of temperature dependence of the fluorescence yield and activation energy. Thus, recombinant Oryza phyA/PΦB is similar but not identical to phyA″. The data demonstrate that the low-abundance–fraction plant phyA (phyA″) comes from the same gene as the major (phyA′) fraction. Because both endogenous phyA fractions differ from the phytochrome expressed in yeast, they appear to be posttranslationally modified and/or bound to partner proteins or cellular substructures. However, the character of the presumed chemical modification is different in phyA′ and phyA″ and its extent is more profound in the case of the former.