Histone variants contribute to the organization of chromatin structures and regulation of genome functions through their deposition into nucleosome. Histone variant H2A.Z, one of the H2A variants, is evolutionarily conserved. H2A.Z is deposited into nucleosome as H2B-H2A.Z histone heterodimer, and this deposition is mediated by an ATP-dependent chromatin-remodeling complex termed SWR1 in budding yeast and SRCAP in vertebrates. The deposition of H2A.Z regulates transcription, DNA damage repair, and chromosome segregation. While the presence of H2A.Z is conserved among eukaryotes, its functions in eukaryotes have not been analyzed. To approach the molecular evolution of H2A.Z, we firstly expressed vertebrate H2A.Z (vH2A.Z) in yeast H2A.Z (yH2AZ) deletant. However, vH2A.Z was not deposited into yeast nucleosome and did not rescue phenotypic defects in the yH2A.Z deletant. When yH2A.Z and vH2A.Z structure are compared, they are very similar in the sequence recognized by SWR1 and SRCAP. On the other hand, the sequence interacting with H2B histone is not conserved between them. This observation raises a possibility that the intermolecular interaction mode between H2A.Z and H2B, which is required for the deposition of H2A.Z into nucleosome, is not conserved between yH2A.Z and vH2A.Z. To test this hypothesis, we expressed a vH2B-vH2A.Z fusion histone in the yH2A.Z deletant. This vertebrate fusion histone was successfully deposited into yeast nucleosome in a SWR1 complex-dependent manner, and it partly complemented phenotypic defects in the yH2A.Z deletant. This observation suggests that the deposition machinery and functions of yH2A.Z and vH2A.Z are evolutionarily conserved. We expect that the vH2B-vH2A.Z fusion histone contributes to further analysis of epigenetic regulation by H2A.Z and its evolutionary conservation.