Isoprenoid quinones are molecules that have a major role in bioenergetics as they shuttle electrons across the respiratory chains of most living organisms. Different types of quinones can be discriminated by their mid-point redox potential. This potential determines respiratory enzymes with which quinones function, accessible respiratory substrates and, ultimately, the environment in which organisms can live. In Proteobacteria, the two main quinones are menaquinone (MK), a low potential quinone (~-70 mV) and ubiquinone (UQ), a high potential one (~+100 mV). So far, UQ has been considered to be well adapted for aerobic respiration, while MK would rather be involved in anaerobic respiration in O2-limited contexts. However, our team recently discovered an O2-independent biosynthetic pathway for UQ production, while the classical pathway depends on the presence of O2 [1]. It was shown that this O2-independent pathway is crucial for anaerobic respiration (denitrification) in Pseudomonas aeruginosa [2]. Thus, these discoveries challenge the respective assumed physiological roles and origins of MK and UQ pathways in Proteobacteria. In this study, we systematically investigated quinone production potential across the Proteobacteria phylum. In this prospect, an annotation pipeline assisted by phylogeny was designed in order to infer the presence of the different quinones biosynthetic pathways existing in this phylum (MK, UQ and rhodoquinone (RQ)) and was applied on a large set of over 2500 complete genomes. Particular attention was paid to the genes specific of the UQ O2-independent pathway, ubiT, -U and –V, which tend to co-localize along genomes. We addressed more particularly the question of their genetic architecture and regulation. Altogether, this large-scale study gives us more insights to propose an evolutionary scenario of the quinones pathways. It also invites us to revisit the classical view of the respective physiological roles of the respiratory quinones found in Proteobacteria.