Protozoan parasites compose a large group of ubiquitous unicellular eukaryotic organisms that closely interact with, and frequently reside within, a larger host. These parasitic protists rely on their host for nutrients, energy, and biomaterials. The host–parasite interaction is complex, as parasites strive to achieve a delicate balance of survival and replication without inducing host death. The host, in turn, tries to protect itself by various means including activation of death pathways in order to limit parasite spread. Therefore, successful parasites have developed highly evolved tactics in order to avoid host immune recognition and intracellular killing and subvert the host to their needs. To this end, various mechanisms of hijacking of host processes via parasite-derived or secreted effectors have been described. It has recently come to light that parasites also induce alterations to the host epigenomic landscape. Changes in host DNA methylation, histone posttranslational modifications, nucleosome positioning, chromatin assembly, and regulation of transcription have been noted in the parasitized host. To date, only a few parasite-derived effectors have been shown to directly modify host chromatin, and it remains to be elucidated whether parasite-induced alterations to the host epigenomic landscape are brought on specifically by parasites or are due to the host response. Finally, while various parasites target different components of host epigenomic landscape, common themes in subversion of host pathways and process emerge. We aim to review what is known about parasite modulation of host epigenome and touch on some conserved themes in this host–parasite interplay.