Myeloproliferative neoplasms (MPNs), which includes polycythaemia vera (PV) and essential thrombocythaemia (ET), are bone marrow disorders that give rise to a high production of red blood cells and platelets leading to thrombosis and haemorrhage. Hydroxyurea (HU), is the first line treatment for high-risk PV and ET patients since it effectively reduces the haematocrit, platelets and white blood cells counts. Mechanistically, HU acts by inhibiting the ribonucleotide reductase enzyme, blocking the cell cycle which can lead to cell death. However, additional effects of HU have also been observed which are unlikely related to this mechanism. Therefore, I hypothesize that HU has an influence on the epigenome, causing changes in gene expression which contribute to its therapeutic effects. For this, I assayed and analysed DNA methylation and gene expression from two differentially developed and clinically relevant cells types from MPN patients and a MPN mouse model, comparing samples prior to and following HU treatment. I observed that HU mainly changes gene expression and specifically affects DNA methylation at the stem cell level. Interestingly, several genes encoding transcription factors involved in haematopoiesis were also identified as potential mediators of HU effects in both species. Moreover, SPI1 was found to be upregulated and differentially methylated following HU treatment. In addition, several differentially expressed genes and differentially methylated sites were enriched for SPI1 binding sites. Thus, I propose that SPI1 is involved in the pathogenesis of the disease and in the therapeutic effect of HU. Finally, I also provide a list of candidate genes to be further investigated for their role in the therapeutic effect of HU.