The thermal structure of a megadiverse mountain ecosystem in southern Ecuador is examined on the basis of temperature measurements inside the natural mountain forest and at open sites along an altitudinal gradient from 1700m to 3200m. The data is used to calculated maps of monthly average minimum, mean and maximum 2m air temperature for the period 1999-2007, needed by ecological projects. The maps are generated by combining the straightforward detrending technique by using a Digital Elevation Model and satellite-based land cover classification. The results reveal a clear thermal differentiation over the year, partly triggered by the change of synoptic weather situation but also by land cover effects. Thermal amplitudes are particularly low during the main rainy season when cloudiness and air humidity are high but markedly pronounced in the relative dry season when daily irradiance and outgoing nocturnal radiation causes distinct differences between the land cover units. Particularly the lower pasture areas gained by slash and burn of the natural forest exhibit the most extreme thermal conditions while the atmosphere inside the mountain forest is slightly cooler due to the regulating effects of the dense vegetation. Thus, clearing the forest clearly reduces the thermal regulation function (regulating ecosystem services) of the ecosystem which might become problematic under future global warming.