Cellular polyamines of 61 archaeal newly published strains were analyzed by HPLC to evaluate correlation of polyamine profiles to their extremophily and chemotaxonomy. A quaternary branched penta-amine, N⁴-bis( aminopropyl )spermidine, was found in hyperthermophilic Methanocaldococcus and Methanotorris belonging to the family Methanocaldococcaceae but not in the family Methanococcaceae nor any other methanogenic archaeal orders. Hyperthermophilic / extremely thermophilic Palaeococcus, Thermococcus and Pyrococcus of the order Thermococcales ubiquitously contained the branched penta-amine. Mesophilic, extreme halophiles including halo-alkaliphiles, belonging to the order Halobacteriales, contained a trace of spermidine, spermine and agmatine. In the phylum Crenarchaeota, extremely thermophilic Caldisphaera of the provisional order 'Caldisphaerales' contained norspermidine, spermidine and agmatine, and hyperthermophilic Pyrobaculum belonging to the order Thermoproteales contained norspermidine, spermidine, norspermine and spermine, but not any penta-amines. Within the order Desulfurococcales, Desulfurococcus and Ignisphaera contained spermidine, norspermidine, homospermidine, norspermine and spermine, whereas Aeropyrum contained caldopentamine and thermopentamine in addition to these triamines and tetra-amines.