The large components of DNA-dependent RNA polymerases (RNAPs) of Archaea, Bacteria and Eucarya were used as molecular markers for the reconstruction of phylogenetic trees. Preferred phylogenetic trees of the three domains of organisms were determinded by a combination of the three major types of inference methods (pairwise distances, maximum parsimony and maximum likelihood) applying the fuzzy logic data analysis method. The preferred phylogenetic trees for the Archaea and Bacteria show branching topologies which differ significantly from the topologies found using ribosomal RNAs as probes: the tree of the Archaea allows a unique location of a characteristics splitting event replacing the largest RNAP subunit (B) of the thermophilic sulfur archaea by two fragments (B′ and B″) in methanogens and halophiles; the tree of the Bacteria shows the lineage of the extreme thermophile Aquifex pyrophilus at a branching point located far away from the root of this domain — clearly not supporting the hypothesis that hyperthermophilia is a relic of primordial environmental conditions. The preferred branching topology of the universal phylogenetic tree reconstructed from the sequences of the second largest components (B) of the three eucaryal RNAPs (Pol I, Pol II and Pol III), the archaeal RNAP components B or B′ plus B″, respectively, and the bacterial RNAP components, β, confirmed the topology formerly inferred from another set of RNAP components: components A of the eucaryal RNAPs, archaeal components A′ plus A″, and bacterial β′ components. The preferred branching topology of this universal tree is characterized by an internodal stretch separating the archaeal lineage and the lineage of the eucaryal Pols II and Pols III on the one hand, from the bacterial lineage and the lineage of the eucaryal Pols I on the other hand. The latter topology led us to the fusion hypothesis for the formation of the Eucarya .