The variant antigenPlasmodium falciparumerythrocyte membrane protein 1 (PfEMP1), which is expressed on the surface ofP. falciparum-infected red blood cells, is a critical virulence factor for malaria1. Each parasite has 60 antigenically distinctvargenes that each code for a different PfEMP1 protein. During infection the clonal parasite population expresses only one gene at a time before switching to the expression of a new variant antigen as an immune-evasion mechanism to avoid the host antibody response2,3. The mechanism by which 59 of the 60vargenes are silenced remains largely unknown4-7. Here we show that knocking out theP. falciparumvariant-silencingSETgene (here termedPfSETvs), which encodes an orthologue ofDrosophila melanogasterASH1 and controls histone H3 lysine 36 trimethylation (H3K36me3) onvargenes, results in the transcription of virtually allvargenes in the single parasite nuclei and their expression as proteins on the surface of individual infected red blood cells. PfSETvs-dependent H3K36me3 is present along the entire gene body, including the transcription start site, to silencevargenes. With low occupancy of PfSETvs at both the transcription start site ofvargenes and the intronic promoter, expression ofvargenes coincides with transcription of their corresponding antisense long noncoding RNA. These results uncover a previously unknown role of PfSETvs-dependent H3K36me3 in silencingvargenes inP. falciparumthat might provide a general mechanism by which orthologues of PfSETvs repress gene expression in other eukaryotes.PfSETvsknockout parasites expressing all PfEMP1 proteins may also be applied to the development of a malaria vaccine.