Coffee Berry Disease which affects green Arabica coffee (Coffea arabica) berries is caused by the fungus Colletotrichum kahawae and is a major problem in Arabica coffee production in African countries. Breeding for resistance to this disease is therefore to a major priority in these countries avoid intensive chemical usage for its control. Recently, microsatellite and Amplified Fragment Length Polymorphisms (AFLP) markers for a gene conferring resistance to the disease were identified and mapped onto the chromosomal region carrying the gene. To improve the repeatability of the AFLP markers, four of the marker bands were selected for cloning and sequencing to facilitate specific primers to be designed. Three of the resultant primers did not amplify products that exhibited polymorphism characteristic of the parent AFLP bands; but one primer pair amplified a product that dominantly identified the presence of the parent AFLP marker at an optimum temperature of 62°C followed by electrophoresis in agarose. The reliability of the designed primers was confirmed by analysis in 95 plants from a F2 population previously used to map the chromosomal fragment carrying the resistance. The importance of the results in enhancing the utility of the parent AFLP marker in relation to analytical costs and position on the chromosomal fragment is discussed.