<p>There is little information on the involvement of farmers as key stakeholders in the design of successful breeding programs that aim to improve indigenous Tswana sheep production. This study used farmers’ participatory approaches to characterise production systems, breeding practices and trait preferences among farmers raising Tswana sheep in Southern and Central agro-ecological zones (AEZ) of Botswana. A structured questionnaire was administered to 190 farmers. An index-based system was used to rank farmers’ preferred traits and data collected were analysed using SPSS. Demographic data showed that most Southern agro-ecology farmers were unmarried males, possessed secondary education and primarily relied on salaries/wages as household income source. In Central agro-ecology, most farmers were males, widowed, had primary education and livestock sales were the main source of income. Tswana sheep are either kept in extensive or semi-intensive production systems. Most Tswana sheep are kept in extensive production systems and there were no significant differences (<i>P</i> &gt; 0.05) in the most preferred production systems across regions. Most farmers prefer using purebred and crossbred Tswana rams from their own flocks for breeding purposes, which mostly is done throughout the year and is uncontrolled. Farmers from Southern agro-ecology cull sheep with small body size and those in Central region cull sheep based on maladaptation. Keeping sheep for income generation through the sale of animals ranked first across AEZ. The highest-ranking trait preferred amongst Southern region farmers was for economic production traits (large-bodied animals) (0.311) whereas in Central region, preference for adaptation traits ranked highest (0.310). These results are key inputs to designing successful and sustainable community-based breeding programs for indigenous sheep in Botswana.</p>