Bush encroachment is a form of land degradation prominent worldwide, but particularly present in semi-arid areas. In this study, we mapped the spatial distribution of the two encroacher species, Acacia mellifera and Acacia reficiens, in Central Namibia, based on their different phenological behavior. We used constrained principal curves to extract a one dimensional gradient of phenological change from two hyperspectral images taken in different seasons. Field measurements of species composition and cover values were statistically related to bi-temporal differences in hyperspectral vegetation indices in a direct gradient analysis. The extracted gradient reflected the relationship between species composition and cover values, and the phenological pattern as captured by the image data. Cover values of four dominant plant species were mapped and species responses along the phenological gradient were interpreted.