Peat bog lakes represent important ecosystems in temperate and boreal zones. We investigated the seasonal dynamics of the microbial community in two small peat bog lakes, Kuźnik Olsowy and Kuźnik Bagienny, located in western Poland. Fluorescence in situ hybridization analyses revealed that the bacterial community was dominated by Proteobacteria and Actinobacteria, in addition to a substantial number of archaea. An infrared epifluorescence analysis demonstrated that aerobic anoxygenic phototrophs (AAPs) constituted a significant fraction of bacterial plankton (1-19%). All the bacterial groups exhibited large seasonal changes whose course differed between the studied lakes. While chlorophyll had its maximum during winter or early summer, AAPs peaked in summer, when the growth of this group was stimulated by higher irradiance and elevated water temperatures.