The structure of biliproteins is typically characterised by bilin chromophores arranged in linear tetrapyrrolic formation, and the bilins are covalently bound to apoproteins via thioether bonds. Each type of biliprotein has a unique bilin that belongs to it (e.g. phycoerythrobilin is the chromophore of phycoerythrin and phycocyanobilin is the chromophore of phycocyanin).  The bilin chromophores are formed by the oxidative cleavage of a haem ring and catalysed by haem oxygenases at one of four methine bridges, allowing four possible bilin isomers to occur.  In all organisms known to have biliproteins, cleavage usually occurs at the α-bridge, generating biliverdin IXα.
Phycobiliproteins are grouped together in separate clusters, approximately 40nm in diameter, known as phycobilisomes.  The structural changes involved in deriving bilins from their biliverdin IXα isomer determine the spectral range of light absorption.
The structure of biliproteins in insects differ slightly than those in plants and algae; they have a crystal structure and their chromophores are not covalently bound to the apoproteins. Unlike phycobiliproteins whose chromophores are held in an extended arrangement by specific interactions between chromophores and proteins, the chromophore in insect biliproteins has a cyclic helical crystal structure in the protein-bound state, as found in studies of the biliprotein extracted from the large white butterfly.