Chromosome conformation capture (3C/Hi-C)-based methods probe the average 3D organization of genomes, revealing fundamental aspects of chromosome dynamics. However, when applied to prokaryotic and archaeal species the current protocols are expensive, inefficient, and limited in their resolution. We developed a cost-effective approach that allows the exploration of bacterial and archaeal chromosome conformations at the gene or operon level. After validation on the well-studied E. coli and V. cholera bacterial species, generating sub-kilobase resolution contact maps and unveiling previously undetected gene-level chromosomal structures, we applied it to the euryarchaeal species, H. volcanii. Hbt. salinarum and T. kodakaraensis. This approach generated Hi-C matrices at a resolution of up to 1kb, allowing to further explore the diversity of chromosome folding in this kingdom. We show that, in contrast to Crenarchaea, these Euryarchaeal species lack active and inactive compartments, and instead resemble the architecture of bacterial chromosomes. The genomes also display sub-Mb domains and DNA loops. In H. volcanii, these structures are regulated by the archaeal SMC protein, further supporting the ubiquitous role of these complexes in shaping the higher-order organization of genomes in all kingdoms.