Abstract Adaptation to reduced levels of oxygen (hypoxia) is an essential feature of eukaryotic life. Within the animal kingdom, cellular responses are orchestrated by the transcription factor HIF (Hypoxia Inducible Factor) which is regulated by specific 2-oxoglutarate-dependent oxygenases. This family of enzymes also includes histone demethylases, and histone methylation has also been observed to increase in hypoxia. Since histone methylation is associated with gene expression, this has raised questions about whether this also contributes to transcriptional regulation in hypoxia. However, to date pangenomic studies have not been normalised in a way that preserves these bulk changes. Using drosophila chromatin spike-in normalisation, we have shown widespread increases in histone H3K4/9/27/36me3 in hypoxia at almost all gene loci that occur irrespective of whether gene expression is increased or reduced. However, methylation of H3K4me3 and H3K36me3 increases most at direct transcriptional targets of HIF and this is abrogated by inactivation of HIF. Taken together this suggests that global H3 trimethylation increases in hypoxia are widespread and not sufficient to predict transcriptional direction, whereas enhanced H3K4me3/H3K36me3 at direct HIF targets appears consequent to HIF binding and transcriptional engagement.