Polycomb repression controls regulation of hundreds of genes involved in development, signalling or cancer and is mediated by essentially two classes of chromatin-associated protein complexes, the Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). PRC2 trimethylates histone H3 at Lysine 27 and this H3K27me3 epigenetic mark serves as a docking site for the PRC1 protein complex. Drosophila core PRC1 is composed of four subunits, Polycomb (Pc), Posterior sex combs (Psc), Polyhomeotic (Ph), and Sex combs extra (Sce). Each of these proteins has multiple orthologs in vertebrates. In particular, mammalian genomes encode five Pc family members (CBX2, 4, 6, 7 and 8), six Psc family members (BMI1, PCGF1, 2, 3, 5, and 6), three Ph family members (PHC1, 2 and 3) and two Sce family members (RING1 and RNF2) generating an enormous scope for potential combinatorial diversity. In order to identify the corresponding PRC1 genes in zebrafish, homology searches were undertaken and allowed the identification of a total of 19 genes. Using phylogenetic, gene organization and gene location analyses, these genes were classified. The zebrafish genes encoding the PRC1 protein complex include 8 Pc orthologs (cbx2, cbx4, cbx6a, cbx6b, cbx7a, cbx7b, cbx8a and cbx8b), 6 Psc orthologs (bmi1a, bmi1b, pcgf1, pcgf5a, pcgf5b and pcgf6), 4 Ph orthologs (phc1, phc2a, phc2b and phc3) and a single Sce ortholog (rnf2). Our results indicate that the potentially high number of distinct PRC1 protein complexes generated by the components combinatorial appeared early in the vertebrate evolution. In addition to conserved gene organization and syntenies, transcript analyses revealed that transcriptional regulation leading to various isoforms syntheses is also conserved at genes encoding the PRC1 components, highlighting a possible important biological role of these isoforms.