The abstract: The Archaeal Thermococcales order comprises anaerobic hyperthermophilic organisms with some of them additionally barophilic. Based on the phylogeny of their 16S rRNA genes, Thermococcales have been ranked into three genera: Pyrococcus, Thermococcus and Palaeococcus [1]. These archaea all harbor small, fast evolving genomes and a number of integrated or self-replicating mobile genetic elements [2–4]. Due to the combined effort of different teams, several isolates are now genetically tractable and used as valid genetic models to investigate the extremophilic way of life. With our complete genomic sequencing of 69 new Thermococcales genomes, the total number of available Thermococcales genomes is now in excess of 100. The size, quality and completeness of these closed chromosomal sequences is making these organisms one of the most represented archaeal order so far. The complete Thermococcales genomic dataset was analyzed using a number of bioinformatics investigating techniques. The different approaches used in our deep comparative analysis concurred in unambiguously ranking all Thermococcales genomes into six genera differing significantly from the current classification. This pangenomic analysis in the Thermococcales will be combined to the prediction of the metabolic pathways, in order to analyse the distribution of these different metabolic pathways at the scale of pangenomes and to understand the evolutionary history of the different metabolic pathways by discussing their ancestral presence, their acquisition by horizontal transfer events or their loss. These analyzes will make it possible to specify the metabolic particularities of the different species, genera and ancestor of the Thermococcales. The redefinition of the concepts of genus and species proposed here allowed the precise characterization of an entire archaeal order. The principles described in this work could be extended to rank accurately any groups of prokaryotic organisms for which a sufficient number of complete genomic sequences are available.