The presence at specific genomic loci of H3K9me modified histones and a global hypo-acetylation of histones. H3K9me2 and the proteins encompassing a chromodomain that are able to bind to these modified histones are essential for genomic integrity and are localised at centromeres, telomeres and repetitive sequences. Different chromodomain proteins exhibit different binding affinities to specific modified histones. Proteins preferentially binding to Nimorazole H3K9me3 peptides are of the HP1-like family and proteins that have a higher affinity for H3K27me3 peptides are of the Polycomb family. Accordingly, we pulled-down the endogenous TgChromo1 protein as confirmed by Western blot. In this case, the anti-HA antibody recognized the endogenous TgChromo1 after purification on the H3K9me3 beads, whereas no protein was pulled down by the H3 peptides, thereby confirming that the endogenous protein has all the functional characteristics of a genuine HP1-like chromodomain protein. Similar to other HP1-like proteins, we mainly identified TgChromo1 in the insoluble fraction of parasite nuclear extracts, suggesting that this protein belongs to the highly-dense, heterochromatic structure or is associated with the nuclear membrane. As a control for the cellular fractionation, we identified in the same fractions a cytoplasmic resident and a nuclear resident also found associated with chromatin in the insoluble extract. Taken together, the data presented here show that TgChromo1 has all the biochemical features required for a chromodomain protein belonging to the HP1like chromodomain family. The polyclonal antibody raised against the TgChromo1 recombinant protein confirmed these features. This profile is in concordance with the TgChromo mRNA steady state level measured by microarray. Interestingly, the parasites are undergoing a main switch from mother to daughter at the onset of G1, a time where they are more able to egress and invade. TgChromo1 might participate in this switch during the parasite cell cycle by virtue of its own regulated expression and serve as one of the mitotic check-points for exiting budding and entering G1. Interestingly, after the division of the centrosome, the signal given by TgChromo1 is elongated when the newly divided centrosomes are separated. It is worth to notice that this localisation is different than the centromeric Histone variant CenH3 at the same stage. Interestingly, HP1-like chromodomain proteins in other eukaryotes are also localised at the telomeric and subtelomeric sequences, including PfHP1 in P. falciparum. The binding of HP1 to the telomeres is independent of the chromodomain and H3K9me3. The functional reason for this association is not yet understood but TgChromo1 may have a role in tethering those sequences to the nuclear membrane. Since telomeric sequences are not enriched in H3K9me3, it is unclear how TgChromo1 would bind to these regions. Chromodomain proteins have been shown in other eukaryotes to bind indirectly to telomeric sequences through their interaction with other proteins. We also show that the T. gondii nucleus is functionally compartmentalised, with a concentration of Apoptosis Activator 2 heterochromatin at specific positions of the nuclear periphery. In eukaryotes, sub-nuclear compartments, which are not delimited by membranes, arise from the clustering of DNA sequences associated with specific proteins, thereby creating micro-environments that can favour or impede particular enzymatic activities. Furthermore, we demonstrate that T. gondii has the ability to define chromosome territories within its nucleus, and TgChromo1 does not participate in the silencing of developmentally regulated genes.