Conservation of indigenous tree species is crucial for restoration of ecosystems and provision of livelihood support functions among rural communities. However, most tree planting initiatives have promoted exotic species, ignoring native species which populations have for long depended on. This study assessed the indigenous tree species conservation and Use Values in the Kyoga plains and the highland ranges Agro Ecological Zones of Uganda. A semi-structured questionnaire was used to capture primary data from a total of 422 household heads. Data were coded and entered in SPSS statistical package (Version 16). Descriptive statistics were generated to establish the distribution of indigenous trees on farms and tree management options employed by farmers. Chi-square test at 5% probability level was used to assess whether there was any difference in indigenous tree establishment, propagation and management options in the four study districts. The Use Value index technique was used to rank and prioritize 20 indigenous tree species. Most of the local communities in Eastern highland ranges prefer planting and retaining indigenous tree species in crop fields, while deliberate tree planting in the vicinity of family compounds (homestead) was predominant in the Kyoga plains. Indigenous tree species mode of establishment, propagation and management options significantly differed across the four study sites (P<0.05). The overall tree species Use Value Indices generally correspond to the number of uses of a particular tree species and vary between 2.4 and 0.2. Our study findings show rather a narrow range between the highest and least use value, implying that communities generally valued a particular tree species for at least more than one preferred use. Local communities prefer protecting naturally growing indigenous tree seedlings than planting. They facilitate tree regeneration when the benefits of their investment are guaranteed and the economic value such trees can provide to the household. Therefore, while evaluating indigenous tree species for relative importance and use, the end objectives of such evaluation must be critically examined in light of the interest of different tree resource user groups.