Eukaryotic histone variants are involved in a wide range of processes and play a key role in altering nucleosome dynamics to shape the architecture of chromatin. The importance of individual variants has been studied extensively in many eukaryotes. In comparison, we know relatively little about histones in archaea. Despite sequence variation and evidence for potential functional differences between histone paralogs in the same species, whether archaea have histone variants, and therefore the potential for complex histone-based chromatin, has not been comprehensively explored. In this work, I apply structural and sequence-based approaches and present evidence that histone variants exist in archaea. In silico modelling suggests that, similarly to some eukaryotic variants, paralogs in archaea can be identified by unique structural properties. In particular, I describe one such variant, a “capstone”, that can drastically alter histone-based chromatin by limiting oligomerisation. Other paralogs have less extreme structural properties but are shared between species which separated hundreds of millions of years ago, on par with some eukaryotic histone variants. Although there are shared features between the two, histones in archaea have appear to have explored a different sequence space to eukaryotic histones, evolving separately and in parallel.