Worldwide, large areas of the tropics are transformed into simplified ecosystems characterised by altered tree species composition and diversity. Human activities in these landscapes have a strong effect on the land cover and exert a selective force on tree species and functional traits, hereby potentially shaping the distribution of ecosystem services in the landscape. The aim of this study was to asses how the land use determines tree species assemblages, their associated traits and potential ecosystem services, which was studied for 589 systematically sampled locations in the Afromontane highlands of Taita Hills (SE Kenya). Several tree traits were non-random distributed in the human-dominated landscape. For instance, on croplands (70% of the sampled locations) belonged 66.5% of the observed species to the exotic tree species group. This group was characterised by significantly larger seeds and fruits, corresponding with the abundance of many fruit trees. Also three functional traits (i.e. economic function, nitrogen fixation and agroforestry potential) were clearly associated with this group. The cloud forest tree species group and small-leaved indigenous group were significantly more present on woodes sites and homesteads (∼42%). However, no functional traits were unique for both indigenous groups, implying that farmers may exchange them by exotics, which could be catalysed by the loss of local knowledge about indigenous tree resources and benefits. Other indigenous species, including endemic or late-successional species were rare or absent in the matrix and their conservation can only be guaranteed by protecting the remaining indigenous forest fragments.