<p><i>Canarium schweinfurthii</i> (Burseraceae), commonly known as African Elemi, is a culturally and economically significant food tree in tropical Africa, valued for its fruits, medicinal uses, and high-quality timber. Despite its importance and wide distribution, no prior studies have explored the species’ genetic diversity, a crucial component for its conservation and sustainable management. This study aims to develop nuclear microsatellite (SSR) markers and use them to provide the first insights into the spatial genetic structure of <i>C. schweinfurthii</i> populations across West and Central Africa. We selected 48 primer pairs from a large SSR database and tested them for amplification and polymorphism. Thirteen polymorphic loci were retained and used to genotype 98 individuals sampled from four populations in three African countries (Cameroon, Côte d’Ivoire, and Burkina Faso), including both wild and cultivated trees. The 13 markers were highly polymorphic with a number of alleles per locus varying from 6 to 29 (average of 16.54 ± 7.81). The mean <i>F</i>_IS coefficient per population was 0.165 ± 0.070. The genetic differentiation (<i>F</i>_ST) was the lowest between geographically neighboring populations (between the population from Côte d’Ivoire and Burkina Faso, and between the two populations from Cameroon) and was the highest between West African populations and Central African populations. We have not observed any reduction in genetic diversity between the wild and cultivated populations in Cameroon. These new SSR markers provide effective tools to study gene flow and population structure in <i>C. schweinfurthii</i>. The observed genetic patterns offer a foundation for future genomic studies and support the development of targeted conservation strategies for this emblematic African tree.</p>