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Chromodomains are a superfamily of protein domains that are implicated in the modulation of chromatin structures. The chromodomain superfamily can be subdivided into two subfamilies, chromodomains and chromo shadow domains. Chromodomains function to localise proteins to specific sites on chromatin. An NMR structure of a chromodomain has been previously solved. Chromo shadow domains are protein-protein interaction domains. These recruit other chromatin associated proteins to their sites of action. The two domains have sequence similarities and are likely to have similar structures. The basis for their functional divergence is not known. In the present study, an X-ray structure of the chromo shadow domain of fission yeast Swi6 protein was solved to 1.9A. The structure reveals that the chromo shadow domain is a dimer with monomers closely resembling the chromodomain structure. Dimerisation of the chromo shadow domains creates a cleft that is commensurate with peptide binding. Binding studies were carried out to further investigate chromo shadow domain function. Recently, proteins of the Drosophila dosage compensation complex were found to contain divergent chromodomain-like regions. These domains have been noted to have RNA binding properties. Preliminary structural studies were carried out to determine if these domains shared a common fold with chromodomains and chromo shadow domains.