Abstract We have surveyed the morphological diversity of viruses infecting the archaeon Aeropyrum pernix , the most thermophilic species among aerobic organisms, growing optimally at 90 °C, and isolated and characterized a novel virus, Aeropyrum pernix bacilliform virus 1 , APBV1. This is the first virus to be described of the genus Aeropyrum and the archaeal order Desulfurococcales. The virion of APBV1 has rigid bacilliform morphology, about 140 × 20 nm, with one end pointed and the other rounded. It contains highly glycosylated single major protein and three minor proteins. The circular, double-stranded DNA genome comprising 5278 bp is the smallest for known archaeal viruses. None of the 14 putative genes, all on the same DNA strand, shows significant similarity to sequences in the public databases. The APBV1 infection caused neither retardation of host growth nor lysis of host cells, and integration of the viral genome into the host chromosome was not detected. On the basis of unusual morphological and genomic properties, we propose to consider APBV1 as the first representative of a new viral family, the Clavaviridae.