Introduction 279 Chromatin Proteins 280Archaeal Histones 280 Alba 284 Sul7 285 Sul10a 285Topoisomerases 286 Conclusions 286 References 287Extremophile microbiology has matured since the 1970s and 1980s when it was dominated by exploration of “ever-more-extreme” environments and classifying extremophiles, both as isolated organisms and through DNA sequences extracted from the environment. Prokaryotic genome sequencing has facilitated extensive comparison of related genes and gene products in extremophiles and nonextremophiles to complement molecular analyses of the processes necessary for life in extreme environments. Our understanding of prokaryotic chromosome structure has also matured from entangled DNA in a nucleoid to an organized nucleoprotein complex with three-dimensional structure and topology that respond to changes in environmental conditions. This chapter describes the architectural chromosomal (chromatin) proteins in thermophilic archaea from geothermal habitats, compares the DNA-protein complexes formed by these proteins, and discusses the contributions of both architectural proteins and enzymes to chromosome topology.