Simple SummaryPhenotypic variability within and between populations can be assessed using morphometric traits. Therefore, this study investigated morphological differences between different goat populations in two distinct agroecological zones of Burkina Faso. Based on 18 linear body measurements and body weight of the 511 adult female animals sampled, no strict distinction was found between the two populations, meaning that these populations are genetically close. Based on body size, four groups were identified representing the two main breeds expected in these areas (Djallonké and Mossi), their crosses, and the crossbred between Mossi type and the third main breed (Sahelian type) of the country. These different goat morphotypes are the results of farmers breeding practices, specifically uncontrolled mating but also intentional crossbreeding in the search for traits of interest.AbstractIn Burkina Faso, goats are the second most numerous ruminant livestock population, with almost exclusively indigenous breeds being reared in extensive production systems in various agroecological zones. This study was carried out to understand the morphological variation of local goat breeds in the Sudano-Sahelian and Sudanian agroecological zones. A total of 511 adult female animals belonging to two presumed populations (Mossi breed in Sudano-Sahelian zone and Djallonké breed in Sudanian zone) were sampled and body weight as well as a range of linear body measurements, following FAO guidelines, were recorded. The least squares means of body measurements of indicated that Sudano-Sahelian goats have significantly (p< 0.001) larger body measurements than Sudanian goats. Furthermore, relative high variability of the two populations in morphometric traits was observed. Principal Component Analysis (PCA) suggested structure between Mossi breed on one side and Djallonké on the other side, but no strict separation was observed, suggesting that gene flow is occurring among the different populations. A dispersion map with four clusters was built based on the first two factors. The least square means of body measurements ranked the four groups from small to large body size, namely Djallonké, Mossi × Djallonké, Mossi, and Sahelian × Mossi. Gene flow from Sahelian goat into other populations of the country, based on migration of the Fulani ethnic group from the Sahel into areas with Mossi and Djallonké breeds, could explain this configuration and confirms the continuous erosion of genetic identity of these two local breeds. The sustainable use of these adapted local goat genetic resources calls for the promotion of sustainable genetic improvement using participatory breeding approaches.