An 18-month reciprocal peat transplant experiment was conducted between two peatlands in the Czech Republic. Both sites were 100% <i>Sphagnum</i>-covered, with no vascular plants, and no hummocks and hollows. Atmospheric depositions of sulfur were up to 10 times higher at the northern site Velke jerabi jezero (VJJ), compared to the southern site Cervene blato (CB). Forty-cm deep peat cores, 10-cm in diameter, were used as transplants and controls in five replicates. Our objective was to evaluate whether CO₂ and CH₄ emissions from <i>Sphagnum</i> peat bogs are governed mainly by organic matter quality in the substrate, or by environmental conditions. Emission rates and &delta;¹³C values of CO₂ and CH₄ were measured in the laboratory at time <i>t</i>=18 months. All measured parameters converged to those of the host site, indicating that, at least in the short-term perspective, environmental conditions were a more important control of greenhouse gas emissions than organic carbon quality in the substrate. Since sulfate reducers outcompete methanogens, we hypothesized that the S-polluted site VJJ should have lower methane emissions than CB. In fact, the opposite was true, with significantly (<i>p</i><0.01) higher methane emissions from VJJ. Additionally, as a first step in an effort to link C isotope composition of emitted gases and residual peat substrate, we determined whether multiple vertical &delta;¹³C profiles in peat agree. A high degree of within-site homogeneity in &delta;¹³C was found. When a specific vertical &delta;¹³C trend was seen in one peat core, the same trend was also seen in all the remaining peat cores from the wetland. The &delta;¹³C value increased downcore at both CB and VJJ. At VJJ, however, 20 cm below surface, a reversal to lower &delta;¹³C downcore was seen. Based on ²¹⁰Pb dating, peat at 20-cm depth at VJJ was only 15 years old. Increasing &delta;¹³C values in VJJ peat accumulated between 1880–1990 could not be caused by assimilation of atmospheric CO₂ gradually enriched in the light isotope ¹²C due to fossil fuel burning. Rather they were a result of a combination of isotope fractionations accompanying assimilation and mineralization of <i>Sphagnum</i> C. These isotope fractionations may record information about past changes in C storage in wetlands.