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The Andes of Ecuador are known for their outstanding biodiversity but also as the region with the highest deforestation rate in South America. This process is accompanied by accelerating degradation and loss of environmental services. Despite an extraordinary richness in native tree diversity, more than 90% of all forest plantations established in Ecuador consist of exotic species, primarily Eucalyptus spp. and Pinus spp. This is mainly due to the lack of information about the autecological and synecological requirements of the native species. The present study aims at providing basic knowledge on the early height development of native species in comparison to exotics. 12,000 seedlings of exotic and native species were planted in experimental trials at three sites of different successional stages: recently abandoned pastures (Setaria sphacelata), bracken (Pteridium arachnoideum) and shrubs. The results presented in this study refer to the status of the seedlings 3 years after planting. Soil data were revealed from soil core analysis from a total of 1008 soil samples distributed systematically over all plots. Soil chemical data were derived from a subsample of 125 randomly selected soil core sites. Soil properties in the study area emerged to be extremely heterogeneous. More than 60% of all plots presented two or more soil clusters. Soils in general were very poor in plant available N. Soil heterogeneity affected extractable Mn and Mg, dominating vegetation cover in turn affected Mn and P. Differences in soil properties had a strong effect for Eucalyptus saligna and Alnus acuminata. Manual above ground weeding showed species-specific effects: Tabebuia chrysantha and Heliocarpus americanus showed improved height growth, while that of Cedrela montana was reduced. There is evidence that A. acuminata can compete in growth with exotic species. Early successional species and exotics performed best on pasture dominated sites. Height growth of the mid-successional species C. montana was facilitated by bracken fern under certain soil conditions, and shrubs facilitated growth of T. chrysantha. The results indicate that reforestation with native species in Ecuador is possible but requires intensive consideration of interactions with soil properties and accompanying vegetation. Macroscopic soil core analysis can be a suitable instrument for detecting small-scale variation of soil properties. Nevertheless, a characterisation of both small-scale variation as well as variation on higher spatial scales, for instance by aerial photographs, is essential for effective planning of reforestation measures in the Andes.