The year-to-year variations of vertical distribution and biomass of anoxic phototrophic bacteria were studied during ice periods 2003–2005 and 2007–2008 in meromictic lakes Shira and Shunet (Southern Siberia, Russian Federation). The bacterial layers in chemocline of both lakes were sampled with a thin-layer hydraulic multi-syringe sampler. In winter, biomass of purple sulphur bacteria varied considerably depending on the amount of light penetrating into the chemocline through the ice and snow cover. In relatively weakly stratified, brackish Shira Lake, the depth of chemocline varied between winters, so that light intensity for purple sulphur bacteria inhabiting this zone differed. In Shira Lake, increased transparency of mixolimnion in winter, high chemocline position and absence of snow resulted in light intensity and biomass of purple sulphur bacteria exceeding the summer values in the chemocline of the lake. We could monitor snow cover at the lake surface using remote sensing and therefore estimate dynamics and amount of light under ice and its availability for phototrophic organisms. In Shunet Lake, the light intensities in the chemocline and biomasses of purple sulphur bacteria were always lower in winter than in summer, but the biomasses of green sulphur bacteria were similar.