Significance Chromatin in eukaryotes is built around histone–DNA complexes, which act as platforms for the integration of regulatory information. Different layers of information are integrated in a combinatorial fashion, for example by exchanging core histones for variants with different properties. We show that histone variants also exist in archaea. In particular, we identify unique archaeal variants that act as capstones, preventing extension of histone–DNA complexes. Importantly, we show that some archaeal histone variants are ancient and have been maintained as distinct units for hundreds of millions of years. Our work suggests that complex combinatorial chromatin that uses histones as its building blocks exists outside eukaryotes and that the ancestor of eukaryotes might have already had complex chromatin.