AbstractPhycobiliproteins are homologous chromoproteins which constitute the phycobilisomes, the light harvesting complexes of the photosynthetic apparatus in cyanobacteria, rhodophyta and cryptophyta. In the present work, phycocyanin (PC) and Phycoerythrin (PE) from a Nostoc species are proposed as protein markers for electrophoretic techniques. Phycocyanin is a blue‐colored phycobiliprotein; it carries phycocyanobilin as chromophoric group and is composed of two subunits, α and β, with Mr of 14000 and 17000, respectively. In contrast, the PE subunits, having a similar Mr of 21000, are deep rose chromoproteins and carry phycoerythrobilin residues. Both low molecular weight phycobiliproteins are also suitable for monitoring protien blotting and the focusing time of protein samples during isoelectric focusing as internal markers. The PE subunits which form a single broad band after sodium dodecyl sulfate‐polyacrylamide gel electrophoresis have different isoelectric points, and they form two visible bands when they reach their isoelectric point. The phycobilisomes constitute up to 50% of the total protein in cyanobacteria and their content in PC or PE can be up‐ or down‐regulated by using different light conditions (chromatic adaptation).