Coffee provides one of the most widely drunk beverages in the world, and is a very important source of foreign exchange income for many countries. Coffea arabica, which contributes over 70 percent of the world's coffee productions, is characterized by a low genetic diversity, attributed to its allopolyploidy origin, reproductive biology and evolution. C. arabica has originated in the southwest rain forests of Ethiopia, where it is grown under four different systems, namely forest coffee, small holders coffee, semi plantation coffee and plantation coffee. Genetic diversity of the forest coffee (C. arabica) gene pool in Ethiopia is being lost at an alarming rate because of habitat destruction (deforestation), competition from other cash crops and replacement by invariable disease resistant coffee cultivars. This study focused on molecular genetic diversity study of forest coffee populations in Ethiopia using PCR based DNA markers such as random amplified polymorphic DNA (RAPD), inverse sequence-tagged repeat (ISTR), inter-simple sequence repeats (ISSR) and simple sequence repeat (SSR) or microsatellites. The objectives of the study are to estimate the extent and distribution of molecular genetic diversity of forest coffee and to design conservation strategies for it’s sustainable use in future coffee breeding. In this study, considerable samples of forest coffee collected from four coffee growing regions (provinces) of Ethiopia were analysed. The results indicate that moderate genetic diversity exists within and among few forest coffee populations, which need due attention from a conservation and breeding point of view. The cluster analysis revealed that most of the samples from the same region (province) were grouped together which could be attributed to presence of substantial gene flow between adjacent populations in each region in the form of young coffee plants through transplantation by man. In addition wild animals such as monkeys also play a significant role in coffee trees gene flow between adjacent populations. The overall variation of the forest coffee is found to reside in few populations from each region. Therefore, considering few populations from each region for either in situ or ex situ conservation may preserve most of the variation within the species. For instance, Welega-2, Ilubabor-2, Jima-2 and Bench Maji-2 populations should be given higher priority. In addition, some populations or genotypes have displayed unique amplification profiles particularly for RAPD and ISTR markers. Whether these unique bands are linked to any of the important agronomic traits and serve in marker assisted selections in future coffee breeding requires further investigations
