Improving the management of goat in rural areas and enhancing its ability to alleviate smallholder poverty requires a better understanding of the existing production systems. This study has been undertaken to characterize the diversity of goat farming systems and identify major constraints and opportunities for their sustainability in two agro-ecological zones of Burkina Faso, namely Sudano-Sahelian and Sudanian, as input for community-based breeding programs. Therefore, data of 372 goat keepers and their herd characteristics were collected in a questionnaire. Two quantitative and 12 qualitative variables were used to perform multiple correspondence analysis and hierarchical cluster analysis. The results indicated that farmers were largely illiterate, with men slightly outnumbered by women. The surveys were divided into 3 clusters. The first 2 clusters were composed of sedentary agropastoral systems. These 2 clusters, which include over 85% of all respondents, represented subsistence crop and livestock productions. Livestock is reared for multiple purposes including income, meat, manure, saving and socio-cultural reasons. The third and smallest cluster (14.5%) was composed entirely of Fulani people in both areas Sudano-Sahelian (85%) and Sudanian (15%). This cluster was the only one containing transhumant production system, with 85% of these farmers practicing seasonal mobility of their herds. Fifteen constraints of goat production were identified, the main ones including conflicts, feed shortage, diseases, lack of workforce and abortions. Although our results showed diversity on goat farming systems among identified groups. Given the lack of formal breeding scheme and institutional support, community-based breeding approaches, which harness the indigenous knowledge and farmers' full commitment, should be explored to improve smallholder production system while conserving genetic diversity.