The genus Pyrococcus consists of approximately 12 described species that are Archaea with optimal growth temperatures near to 100 oC. Pyrococcus furiosus and Pyrococcus woesei were both isolated from marine sediments in the same Italian Vulcano Island site. Insertion sequences (ISs) were identified in the genomes of P. furiosus and P. woesei. Specific primers to differentiate between the types of IS elements were developed. Nucleotide sequence of the rDNA operon (AY519654) from P. woesei was sequenced for the first time. Extensive co-linearity between the genomes of the P. woesei and P. furiosus was demonstrated using radio-labeled IS element sequence probes. A recent transposition event that disrupted the napA gene of P. woesei was revealed. The presence of a type I IS element was observed in the same context in the genomes of P. furiosus and P. woesei. The strains were proposed to be sub sp. of P. furiosus, based on their identical rDNA operon sequence and the presence of IS element markers. The ISs have putative archaeal promoters with a 5' TATA box "boxA". Full length IS mRNAs were detected. Evidence for programmed translational frameshift sites that might limit the translation of the full length transposase was found. Two functional programmed translational frameshift sites were identified in E. coli. The mechanism of frameshifting identified in context 79 in the tnp-I sequence appears to be a novel -2 mechanism, in that the shift site is part of a -1 frameshifting motif. The possible role of a putative ribosome binding site (rbs) observed in context 79, that correlates with high frameshift levels, is discussed.