This study compares MODIS NDVI 16-day (250 m) time series, acquired by Terra and Aqua platforms, for monitoring the phenological cycle of larch and grasslands in an alpine environment. The accuracy of MODIS 250 m Terra and Aqua phenological metrics was evaluated for larch forests through comparison with field data. At regional level it was carried out a correlation analysis between the mean dates of start and end of season detected from MODIS Terra and Aqua in different years. Regional maps of start and end of season were derived from MODIS data and the interannual phenological variability of both ecosystems was evaluated. Annual anomalies of the beginning of the growing season, obtained from satellite data, were related with air temperature anomalies, computed from meteorological stations, to evaluate the effects of recent climate variability on the vegetation phenological cycle. Comparison with field phenological observations showed that the start and the end of phenological cycle can be accurately determined from MODIS Terra and Aqua data and that an increase/decrease of 1°C in spring temperature lead to about 10 days in advance/ delay of the start of the growing season.