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Rapid changes in land-use in the Combretum–Terminalia woodlands of northwestern Ethiopia are mainly due to the increases in commercial farming and immigration. We used integrated ecological and social data collection techniques, including subdivision of the vegetation zone, vegetation survey, focus group discussions and key informant interviews, to identify genecological zones and set criteria for selection of viable populations of Boswellia papyrifera (Del.) Hochst in Ethiopia for conservation. Interviews of senior experts were supported with a rating method and involved 43 respondents and focused on identifying and weighting criteria and indicators of selection in a participatory way to prioritize populations for conservation. Using mean annual rainfall data, we reclassified the Combretum–Terminalia woodland vegetation region into three moisture zones (wet, moist and dry), and designated them as genecological zones for B. papyrifera conservation. A total of 35 woody species were identified at Lemlem Terara site in Metema district, and the Shannon diversity index and evenness were 2.01 and of 0.62, respectively. There were 405 adult trees, and 10 saplings and 3314 seedlings per ha. The trees were medium-sized with overall mean diameter at breast height (dbh) of 16.9 (±9.5) cm. Seedling recruitment was poor due to grazing, crop production and fire incidences. Through a multi-criteria decision analysis, five criteria and 20 quantitative indicators were identified and weighted to prioritize populations for conservation. These criteria in their descending order of importance are (1) forest ecosystem health and vitality, (2) forest cover and population structure of B. papyrifera, (3) productive function of the forest, (4) biological diversity in the forest, and (5) socioeconomic benefits of the forest to communities. Multivariate tests in the general linear model revealed significant differences among researchers and nonresearchers in rating the criteria and indicators, but not among foresters and nonforesters. Hence, participatory multi-criteria decision analysis should involve people from various institutions to rectify decisions on conservation of the species. Careful evaluation of the investment policy environment and engaging those government bodies that are responsible to allocate the dry forests for commercial farming is recommended before the proposed criteria are applied to select populations for conservation, thus ensuring subsequent use of the outcomes of such exercises and better reconciling conservation and agricultural production increment goals.