The three-dimensional organization of chromatin has an important role in genome functions. In bacteria and eukaryotes, structural maintenance of chromosomes (SMC) protein complexes such as condensin mediate higher-order chromosome organization. However, many archaea do not have condensin, and the establishment and maintenance of archaeal chromosome conformation was not well understood. Takemata, Samson and Bell used chromosome conformation capture to investigate the spatial organization of the chromosomes of Sulfolobus species. They found that the chromosomes are organized into two compartments with higher and lower gene expression activities — the A compartment and B compartment, respectively. This non-random chromosome organization was established by coalescin, a novel Sulfolobus-encoded SMC protein. Coalescin is enriched in the B compartment and binds to less active genes, thus maintaining the compartmentalization of the archaeal chromosome.