Angiosperm genome sizes (GS) range ~2400-fold and comprise genes and their regulatory regions, repeats, semi-degraded repeats, and ‘dark matter’. The latter represents repeats so degraded that they can no longer be recognised as repetitive. In exploring whether the histone modifications associated with chromatin packaging of these contrasting genomic components are conserved across the diversity of GS in angiosperms, we compared immunocytochemistry data for two species whose GS differ ~286-fold. We compared published data forArabidopsis thalianawith a small genome (GS = 157 Mbp/1C) with newly generated data fromFritillaria imperialis, which has a giant genome (GS = 45,000 Mbp/1C). We compared the distributions of the following histone marks: H3K4me1, H3K4me2, H3K9me1, H3K9me2, H3K9me3, H3K27me1, H3K27me2, and H3K27me3. Assuming these histone marks are associated with the same genomic features across all species, irrespective of GS, our comparative analysis enables us to suggest that while H3K4me1 and H3K4me2 methylation identifies genic DNA, H3K9me3 and H3K27me3 marks are associated with ‘dark matter’, H3K9me1 and H3K27me1 mark highly homogeneous repeats, and H3K9me2 and H3K27me2 mark semi-degraded repeats. The results have implications for our understanding of epigenetic profiles, chromatin packaging and the divergence of genomes, and highlight contrasting organizations of the chromatin within the nucleus depending on GS itself.