Methylation of H4K20 (Lys(20) of histone H4) plays an important role in the regulation of diverse cellular processes. In fission yeast, all three states of H4K20 methylation are catalysed by Set9. Pdp1 is a PWWP (proline-tryptophan-tryptophan-proline) domain-containing protein, which associates with Set9 to regulate its chromatin localization and methyltransferase activity towards H4K20. The structure of the Pdp1 PWWP domain, which is the first PWWP domain identified which binds to methyl-lysine at the H4K20 site, was determined in the present study by solution NMR. The Pdp1 PWWP domain adopts a classical PWWP fold, with a five-strand antiparallel β-barrel followed by three α-helices. However, it differs significantly from other PWWP domains in some structural aspects that account, in part, for its molecular recognition. Moreover, we revealed a unique binding pattern of the PWWP domain, in that the PWWP domain of Pdp1 bound not only to H4K20me3 (trimethylated Lys(20) of histone H4), but also to dsDNA (double-stranded DNA) via an aromatic cage and a positively charged area respectively. EMSAs (electrophoretic mobility-shift assays) illustrated the ability of the Pdp1 PWWP domain to bind to the nucleosome core particle, and further mutagenesis experiments indicated the crucial role of this binding activity in histone H4K20 di- and tri-methylation in yeast cells. The present study may shed light on a novel mechanism of histone methylation regulation by the PWWP domain.