Abstract Phytochrome in the cryptophytic kingdom of blue-green, red and green algae is described in this review, in terms of molecular properties and biological function. With the recent discovery of Synechocystis phytochrome, the concept of phytochrome being a light-regulated kinase was revitalized, even though phytochrome-dependent kinase activity in eukaryotic cells is still a matter of controversy. Possibly, the phytochrome signal transducing machinery has been adopted in plants through endocytobiosis of cyanobacteria and chloroplast development. Phytochrome function in conjugating green algae, namely Mougeotia and Mesotaenium, has been studied in details. Unexpectedly, a domain at the C-terminal end of both pigments was discovered to be reminiscent of a mcirotubule-associated protein, not a trans-membrane protein. Also in Mougeotia, the cylindrical scaffold of microtubules was found to be light-regulated, mediated by calcium-calmodulin. Thus, the microtubular scaffold and associated proteins appear worthwhile to be considered as candidates to bridge the gap in the transduction chain between the formation of the “tetrapolar” phytochrome gradient in the Zygnematales and chloroplast orientation with respect to light. In a mono-molecular or multi-molecular “reaction unit”, the blue-light photoreceptors in discussion need to be obeyed here as well, for competition to or coaction with phytochrome, both handling the chloroplast rotation through consistent control of the actin-myosin motor apparatus.