Microbial oxygenic photosynthesis in thermal habitats is thought to be performed by Bacteria in circumneutral to alkaline systems (pH > 6) and by Eukarya in acidic systems (pH < 3), yet the predominant oxygenic phototrophs in thermal environments with pH values intermediate to these extremes have received little attention. Sequencing of 16S and 18S rRNA genes was performed on samples from twelve hot springs in Yellowstone National Park (Wyoming, USA) with pH values from 3.0 to 5.5, revealing that Cyanobacteria of the genus Chlorogloeopsis and algae of the genus Cyanidioschyzon (phylum Rhodophyta) coexisted in ten of these springs. Cyanobacteria were detected at pH values as low as 3.0, challenging the paradigm of Cyanobacteria being excluded below pH values of 4.0. Cyanobacterial 16S rRNA genes were more abundant than rhodophyte 18S rRNA genes by up to 7 orders of magnitude, with rhodophyte template abundance approaching that of Cyanobacteria only at the most acidic sites. Light-driven carbon fixation was observed at two sites where chlorophyll a was detected but not at two other sites where chlorophyll a was not detected. Collectively, these observations suggest that many of the rhodophyte 18S rRNA gene sequences were from inactive cells. Fluctuations in the supply of meteoric water likely contributes to physicochemical variability in these springs, leading to transitions in photosynthetic community composition. Spatial, but perhaps not temporal, overlap in the habitat ranges of bacterial and eukaryal oxygenic phototrophs indicates that the notion of a sharp transition between these lineages with respect to pH is unwarranted.