Structural Maintenance of Chromosomes (SMC) ATPases are key regulators of 3D genome architecture in diverse organisms. Although SMC homologs are widely found in the domain Archaea, their roles in archaeal genome organization remains largely unknown. Recently, we and others have successfully applied the Chromosome Conformation Capture (3C) sequencing methods Hi-C and 3C-seq to various archaeal model organisms. These studies have revealed that archaeal SMC proteins exhibit both common and unique functional properties compared to those in eukaryotes and bacteria. Here, we present a high-resolution 3C-seq protocol that is optimized for mapping genome organization in the hyperthermophilic model archaeon Thermococcus kodakarensis.