Histone H4 is a protein subunit of nucleosomes in eukaryotes and play crucial roles in DNA package and in regulation of gene expression by covalent modification. A viral histone H4 is encoded in a polydnavirus called Cotesia plutellae bracovirus (CpBV). The viral H4 (CpBV-H4) is highly homologous with other H4 proteins except 38 extended residues in N terminus. Its expression alters insect gene expression and suppresses immune and development. In this study, CpBV-H4 was expressed in a natural host, Plutella xylostella, and its suppressive activity on host gene expression was detected by suppressive subtractive hybridization (SSH) technique. SSH targets, of which expressions were down-regulated by CpBV-H4, were read by 454 pyrosequencing and annotated using the published P. xylostella whole genome. Resulting targets were assigned to most GO functional categories. Two chromatin remodeling factors were included in the SSH targets. Lysine demethylase (Px-KDM) of P. xylostella was highly expressed during entire larval period in all tested tissues. However, the suppression of Px-KDM expression by a specific RNA interference (RNAi) did not affect immune response, but significantly impaired the larval development. SWI/SNF of P. xylostella (Px-SWI/SNF) was expressed in all developmental stages. Its RNAi did not affect larval development, but led to significant alteration in adult metamorphosis. CpBV-H4 suppressed expressions of both Px-KDM and Px-SWI/SNF, but its truncated mutant lacking in the extended N-terminal tail did not. These results suggest that the developmental alteration in P. xylostella parasitized by C. plutellae can be caused by an epigenetic control of CpBV-H4 against chromatin remodeling factors.