Pinus canariensis is endemic to the western Canary Islands (NW coast of Africa), where it forms forest spanning an altitude from 500 to 2500 m. There are dramatic changes in environmental conditions (temperature, moisture and solar radiation) over short distances due to this elevation gradient in the Canary Island pine forest. Those differences in environmental conditions may lead to asynchronous flowering times among elevations. In this study we used nuclear and chloroplast microsatellites to characterize the genetic structure of two altitudinal transects on the southern slopes of Tenerife Island to test for genetic isolation among altitudes. Although significant differentiation among sites was detected, this differentiation was very low (FST=0.013 with chloroplast markers, FST=0.019 with nuclear markers) and appeared to be unrelated to altitude. The contrasting results between nuclear and chloroplast markers are also discussed in terms of statistical accuracy of markers and genome inheritance.