Seasonal population fluctuations and diversity of anoxygenic phototrophs and cyanobacteria at the Sulphur Mountain thermal springs, Banff, Canada were investigated and compared to drastic population changes of the endangered snail Physella johnsoni. The microbial community revealed new species of anoxygenic phototrophic bacteria with novel spectral and morphological characteristics. Major mat-forming organisms included densely growing Thiothrix-like species, oxygenic phototrophs of the genera Spirulina, Oscillatoria, and Phormidium and purple nonsulfur bacteria Rhodobacter, Rhodopseudomonas and Rhodomicrobium. Aerobic anoxygenic phototrophs comprised a significant portion, upwards of 9.6 × 10⁴ CFU/cm² of mat or 18.9% of total aerobic heterotrophic isolates, while PNSB and purple sulfur bacteria were quantified at maximum abundance of 3.2 × 10⁵ and 2.0 × 10⁶ CFU/cm² of mat, respectively. Photosynthetic activity revealed incredibly productive carbon fixation rates, averaging 40.5 mg C/cm²/day at one studied spring system. A temporal mismatch was observed for mat area and available organics to the fluctuation of P. johnsoni population in a tracking inertia manner. Mat chlorophyll a content appeared directly proportional to snail numbers making it an appropriate indicator of population. This survey of the Sulphur springs microbial communities suggests that phototrophic species are among the main determinants to the proliferation of P. johnsoni.