Globally, preferences for fruit trees have fluctuated over time. However, the most desirable attribute of cultivated fruit tree species has not been consistent across all species and locations. Therefore, the purpose of this study was to determine farmers' preferences for fruit tree species and the associated problems they face in four different study sites, categorized by gender and family size. Equal sampling techniques were used in each selected study site, resulting in a total of 120 household heads participating in structured interviews. The data collected was then analyzed using SPSS version 26 software, utilizing the Mann-Whitney U and Kruskal-Wallis tests. Across the study sites, a total of fourteen fruit tree species from ten families were found to be preferred. The preference for fruit trees based on gender showed no significant difference among respondents between kebeles per woreda. However, the preference for fruit trees based on family size showed a significant difference between kebeles per woreda. The number of species preferred for their subsistence value was twice as large as those preferred for commercial reasons. The proportions of these preferred species and the percentage of observed problems with fruit trees varied significantly across the studied sites. Of all the interviewed household heads, 70% in Fenika, 36.6% in Kite, 66.6% in Shesheka, and 50% in Kometa kebeles encountered severe problems during fruit tree planting. The most common problems identified were disease or pest infestation, lack of expert support, land availability, knowledge, and access to seedlings. In order to address these issues, it is important to utilize indigenous knowledge and scientifically tested research approaches to alleviate the factors that influence farmers' preferences.