UNLABELLED: Chromatin structure plays a central role in the regulation of Epstein-Barr Virus (EBV) latency. The histone variant H2A.Z.1 has been implicated in chromatin structures associated with initiation of transcription and DNA replication. Here, we investigate the functional role of H2AZ.1 in the regulation of EBV chromatin, gene expression and copy number during latent infection. We found that H2A.Z.1 is highly enriched with EBNA1 binding sites at IMPORTANCE: Cellular factors the restrict latent viral reactivation are of fundamental importance. We have found that the cellular histone variant H2A.Z functions in cooperation with the Epstein-Barr Virus (EBV) latency maintenance protein EBNA1 to establish a stable epigenome and restrict lytic cycle reactivation during latency. We show that H2A.Z co-occupies EBNA1 binding sites on the EBV and host genome, and that depletion of H2A.Z leads to robust reactivation of EBV from latency. H2A.Z is important for the function of EBNA1 at the origin of plasmid (oriP) replication and establishing EBV epigenetic marks. H2A.Z binds with EBNA1 at cellular binding sites and controls the expression of cellular genes in the cMyc and mTORC1 pathways that are also implicated in control of EBV latency.