To obtain the genome sequence of Ostreid herpesvirus 1 (OsHV-1) infected Zhikong scallop (Chlamys farreri) in 2001 (ZK2001), and its phylogenetic relationship with the other reported variants, the genome DNA of the ZK2001 variant was firstly enriched through long-range PCR, and sequenced with Illumina Hiseq 2500 PE250 platform. Then the variation and phylogenetic relationship between ZK2001 and the other reported variants were analyzed. 8 scaffolds were obtained after assembly. Genome variation analysis indicated that there were 328 SNPs between ZK2001 and the reference genome. SNPs and insert/deletion were the main cause of genome differentiation. Phylogenetic inference indicated that ZK2001 variant was more closely related to OsHV-1 variants isolated from China than those from Europe. These results indicated that genetic differentiation had occurred as a result of geographic isolation. This study indicated genomic DNA of OsHV-1, which had been frozen for a long time, could be enriched with long-range PCR and used for high-throughput sequencing. The genomic data of different OsHV-1 variants will be necessary for further study of the genetic variation, evolution and phylogenetic analysis of the virus.