The primary structure (amino acid sequence) is highly conserved among OCP sequences, and the full-length protein is usually co-located on the chromosome with a second open reading frame that was later characterized as the FRP. Often, biosynthetic genes for ketocarotenoid synthesis (e.g., CrtW) are nearby.  These conserved functional linkages underscore the evolutionary importance of the OCP style of photoprotection for many cyanobacteria.
The first structure determination of the OCP coincided with the beginning of the genome sequencing era, and it was already apparent in 2003 that there is also a variety of evolutionarily related genes which encode proteins with only one of the two domains present in OCP.  The N-terminal domain (NTD), "Carot_N", is found only in cyanobacteria, but exhibits a considerable amount of gene duplication.  The C-terminal domain (CTD), however, is homologous with the widespread NTF2 superfamily, which shares a protein fold with its namesake, nuclear transport factor 2, as well as around 20 other subfamilies of proteins with functions as diverse as limonene-1,2-epoxide hydrolase, SnoaL polyketide cyclase, and delta-5-3-ketosteroid isomerase (KSI).  Most, if not all, of the members of the NTF2 superfamily form oligomers, often using the surface of their beta sheet to interact with another monomer or other protein.
Bioinformatic analyses carried out over the past 15 years has resulted in the identification of new groups of carotenoid proteins:  In addition to new families of the OCP, there are HCPs and CCPs that correspond to the NTD and CTD of the OCP, respectively.  Based on the primary structure, the HCPs can be subdivided into at least nine evolutionarily distinct clades, each binds carotenoid. The CCPs resolve into 2 major groups, and these proteins also bind carotenoid.  Given these data, and the ability to devolve OCP into its two component domains while retaining function has led to a reconstruction of the evolution of the OCP.