Hyperthermophilic archaea are rarely found in conditions of active growth in their natural environments. Many hyperthermophiles are believed to be dormant under steady-state conditions. The stationary phase is considered a crucial growth stage for understanding cells' survival strategies in their natural habitats. Intracellular polyamines are expected to play a vital role in maintaining the integrity of genomic DNA. However, no study has yet explored the differences in polyamine composition and genomic DNA status between the logarithmic growth phase and the stationary phase. In this study, we investigated the variations in polyamine composition in two types of hyperthermophilic Archaea: Pyrobaculum calidifontis VA1, isolated from a submarine hydrothermal deposit in the Philippines, and Thermococcus kodakarensis KOD1, isolated from a hydrothermal sulfur mine in the Tokara Islands, Japan, during different growth stages. Our analysis focused on scrutinizing the differences in polyamine composition between Thermococcus kodakarensis KOD1 and Pyrobaculum calidifontis VA1, and we examined how these differences affect the structure of genomic DNA.