The cocoa pod borer (CPB) Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae) is one of the major constraints for cocoa production in South East Asia. In addition to cultural and chemical control methods, autocidal control tactics such as the Sterile Insect Technique (SIT) could be a efficient addition to the currently applied control tools for CPB. The SIT is species-specific, and its successful implementation will mainly depend on adequate competitiveness of the sterile males released in the target area. In addition the technique requires an area-wide integrated pest management approach, that would target an entire pest population. Population genetic studies have in the last decades been used to provide information on gene flow between neighbouring insect populations. However, genetic markers would be required for such studies and these were not available for CPB. The aim of the present work was to search for suitable microsatellite loci in the genome of CPB that is partially sequenced. A total of 28,730 primer pairs were found and 192 pairs were selected based on the amplicon size (180-300 nt) and the motif repeats (≥11). They were synthesized and tested against the DNA of C. cramerella. Twelve microsatellites fulfilled all parameters and these were used to analyze moths collected from Indonesia, Malaysia, and the Philippines These loci were also tested against a closely related species, i.e. the lychee fruit borer Conopomorpha sinensis(LFB) from Vietnam. Genetic divergence proved substantial and one diagnostic locus could be characterized. This allowed excluding one CPB individual from Vietnam. A quality control verification process was carried out for both species and 7 microsatellites seemed to be suitable for CPB populations and 11 loci for LFB. The availability of these novel microsatellite loci will provide useful tools for the analysis of the population genetics of CPB, to understand its dynamics and ecology and to assess the level of gene flow between neighbouring populations that would be targeted with an area-wide integrated pest management approach with an SIT component.