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Agroforestry systems are potentially suitable for conservation of tree genetic resources. Farmers around Mt. Kenya usually integrate trees into their farm. Large parts of these trees seem to be of exotic origin, whereas indigenous species have priority for conservation. This study aimed at determining on-farm richness, composition and frequency of indigenous and exotic woody species around Mount Kenya to assess the suitability of farms for the conservation of indigenous tree species. 265 on-farm plots of 0.5 ha size each were selected in 18 different agro-ecological zones by using a stratified sampling scheme. All woody species within the plot were recorded with their local and scientific names. Total species richness was 424 (including 306 indigenous ones), mean richness per plot 16.5 species (including 8.8 indigenous ones). Eight out of the 10 most frequent species were exotic ones with Grevillea robusta from Australia ranking first (found on almost 76% of the surveyed farms). The proportion of indigenous species increased with increasing aridity and temperature. Dominance of exotic species was found at farms of humid mid-and highlands. Ordination analysis revealed that mostly exotic species contributed to separation of farms in the highlands and upper midlands, whereas indigenous species in the lower midlands and lowlands. As the frequencies of most indigenous trees were low, only parts of the surveyed farms can contribute to conservation of tree genetic resources, particularly the less intensively managed farms of the more arid lands. Farmers’ access to knowledge on valuable indigenous tree species and to quality seedlings of these trees need to be improved to increase indigenous species’ frequencies on farms and possibly to replace some of the exotic species in the future.