Structural features that have important implications for the fundamental process of transmembrane proton transfer are examined in the recently published high resolution atomic structures of the reaction center (RC) from Rhodobacter sphaeroides in the dark adapted state (DQAQB) and the charged separated state (D+QAQB-); the latter is the active state for proton transfer to the semiquinone. The structures have been determined at 2.2 Å and 2.6 Å resolution, respectively, as reported by Stowell et al. (1997) [Science 276: 812–816]. Three possible proton transfer pathways (P1, P2, P3) consisting of water molecules and/or protonatable residues were identified which connect the QB binding region with the cytoplasmic exposed surface at Asp H224 & Asp M240 (P1), Tyr M3 (P2) and Asp M17 (P3). All three represent possible pathways for proton transfer into the RC. P1 contains an uninterrupted chain of water molecules. This path could, in addition, facilitate the exchange of quinone for quinol during the photocycle by allowing water to move into and out of the binding pocket. Located near these pathways is a cluster of electrostatically interacting acid residues (Asp-L213, Glu-H173, Asp-M17, Asp H124, Asp-L210 and Asp H170) each being within 4.5 Å of a neighboring carboxylic acid or a bridging water molecule. This cluster could serve as an internal ’proton reservoir‘ facilitating fast protonation of QB- that could occur at a rate greater than that attainable by proton uptake from solution.