We analyzed the testate amoebae communities from two sets of moss samples taken forty years apart (1961 and 2001) in the same locations of a peat bog of the Swiss Jura Mountains. Peat cutting and lateral drainage of Le Cachot bog have caused a clear increase in tree cover, especially near the edges. Changes affecting herbaceous plants, mosses, or soil organisms can be subtle, and may easily be overlooked. We hypothesized that we would see changes in the dominant Sphagnum species and the structure of testate amoebae communities living in the mosses. More specifically, we hypothesized that the frequency of bryophyte and testate amoebae species indicative for dry conditions would increase and that the frequency of species indicative for wet conditions would decrease. The mean testate amoebae species richness per sample decreased from 11.9 to 9.6, but the overall species richness was identical (33 species) in both years. Three species increased significantly in mean relative abundance: Nebela tincta s.l. (+97%), Bullinularia indica (+810%), and Cyclopyxis eurystoma (+100%; absent in 1961), while two species decreased significantly: Assulina muscorum (-63%) and Euglypha compressa (-93%). The testate amoebae communities clearly differed among microhabitat types (hummocks, lawns, hollows), but no overall significant change in the community was detectable between the two sampling dates (Mantel test). These results could signify that changes at the microscopic level had already taken place by 1961 and no further overall significant changes in micro-environmental conditions took place during the 40-year period of this study. This would agree with the faster response time usually attributed to microorganisms and would also imply that the bushes and trees may be poor predictors of the response of microorganisms if they are themselves in a non-equilibrium stage. Other possible causes for the lack of overall differences are discussed.