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A multi-temporal analysis and statistical analysis were applied to examine vegetation index (VI) based vegetation separability based on investigation data from 99 vegetation plots sampled in 2009 and corresponding 10-year timeseries of MODIS EVI and NDVI data of these plots in the Wenquan area, a transition area between permafrost and seasonally frozen soil on the eastern Qinghai-Tibet plateau. The analyses of multi-temporal VI dataset show similar phenological characteristics of all vegetation types during the entire growth season, while they have distinguishable VI values at different periods, namely germination, maturity and senescence periods. Spectral separability between every two vegetation types identified by the Jeffries-Matusita distance statistic is not significant in the growing season, indicating the vegetation classes of this study area not spectrally separable. High intra-class variability of each vegetation type is the primary cause of low separability in different growth periods.