Sixteen new polymorphic microsatellite loci were developed for a tephritid of economic importance in many African countries, Ceratitis cosyra. These markers were tested on field populations from four African countries of its endemic range: Burkina Faso, Tanzania, Burundi and Ethiopia. Low to high polymorphic loci are described (from 3 to 21 alleles/loci), with high variation recorded between countries. Little linkage disequilibrium was detected among all pairs of loci tested (15 out of 120). These new markers will be a useful tool to study the genetic structure of this African species, which is also a fruit fly of quarantine importance for Europe.