Quantitative estimates of the rate of transformation of moss residues of two species (Sphagnum angustifolium and Sphagnum fuscum) in the peat soils (Histosols) were obtained for two oligotrophic bogs with different hydrological conditions in the southern taiga of Western Siberia. The coefficients of decomposition rate (k) significantly differed for the studied species; the decomposition of Sphagnum fuscum proceeded much slower. The most intense decomposition was observed in the first year of transformation (k = 0.06 and 0.16–0.66 for Sph. fuscum and Sph. angustifolium, respectively); then, the rate of moss decomposition decreased. Despite the great amount of fungal mass in the moss residues (exceeding the bacterial biomass by 3–10 times), the rate of the initial decomposition was very low. The hydrological conditions affected the intensity of this process—in the peat of the Kirsanovskoe bog with the low level of bog water, losses of the mass of sphagnum moss were 1.1–1.6 times greater as compared to those in the Bakcharskoe bog. For Sph. angustifolium, the level of bog water was more important than for Sphagnum fuscum, whereas for Sphagnum fuscum, the composition of organic matter played a decisive role in the rate of decomposition of moss residues. The activity of the microflora also depended on the level of bog water, which was manifested in a greater abundance of bacteria in the peat of the Kirsanovskoe bog.