Brown rot on peaches and nectarines caused by Monilinia spp. results in significant economic losses in Europe. Experiments were conducted to study the effects of temperature (0–33 °C) on the temporal dynamics of decay and mycelium development and the subsequent sporulation on peaches and nectarine fruit infected by M. laxa and M. fructicola. The rates of decay and mycelium development increased with temperature from 0 °C to 25 °C for both Monilinia species. At 0 °C, decay was faster for M. laxa (0.20 cm2 days−1) than for M. fructicola (0.07 cm2 days−1); indeed, M. laxa was able to develop mycelia and sporodochia, but M. fructicola was not. At 4 and 20 °C, there were no differences in decay and mycelia development between the two Monilinia species. When temperature increased from 25 to 33 °C, the rates of fungal decay and mycelium development decreased. At 30 and 33 °C, M. fructicola decayed faster (0.94 and 1.2 cm2 days−1, respectively) than M. laxa (0.78 and 0.74 cm2 days−1, respectively) and could develop mycelia and produce sporodochia, whereas M. laxa failed at 33 °C. These results indicated that M. fructicola is better adapted to high temperatures, whereas M. laxa is better adapted to low temperatures. These results can be used to predict the relative importance of the two species during the season at a given site and to improve management strategies for brown rot in areas where both species are present.