We have constructed a genome DNA map of the Antheraea pernyi nucleopolyhedrovirus (AnpeNPV) and used it to identify target genes for deletion in order to improve the newly developed baculovirus expression vector system. Initially, 50 independent PstI fragments of viral DNA were obtained by shotgun cloning, and both termini of each cloned fragment were sequenced. Then, the sequence data were used for homology search against both nucleotide and amino acid sequences of other NPVs in databases. This homology search allowed us to construct a nearly complete restriction map of a viral DNA with several assumed gaps. Four additional PstI fragments covering the gaps were obtained by PCR amplification, and a complete map of a circular viral DNA, which consisted of 54 PstI fragments, was constructed. The map indicated that the AnpeNPV genome is approximately 130.2 kbp in size and possesses high similarity to the Orgyia pseudotsugata multicapsid NPV (OpMNPV) genome in both sequence and arrangement of genes. Utilizing the genome-wide high similarity between AnpeNPV and OpMNPV, we identified two target genes on the map, namely, cathepsin and chitinase genes, whose products have been proved to be involved in the degradation of recombinant proteins and the liquefaction of virus-infected insect tissues. Comparative sequence analysis of the map also revealed the lack of certain OpMNPV open reading frame (ORF) homologs and the presence of ORFs, whose homologs do not exist in OpMNPV but in other group I NPVs, providing an insight into the position of AnpeNPV in the baculovirus phylogeny.