In spite of their importance, the level and distribution of wild Coffea arabica L. in Harrena hasrnnot been extensively examined in depth with molecular markers. The current study wasrnconducted on the wild Arabica coffee of the Harenna Forest of Bale Mountain, southeast part ofrnEthiopian. The levels and distribution of within and among populations genetic diversity of onernhundred wild Coffea arabica L individuals, representing four populations: two from semidisturbedrn(Bale-I and Bale-3) and two from undisturbed (Bale-4 and Bale-6) regions of the forest,rnwere collected and evaluated with Inter Simple Sequence Repeats (ISSR). A total of nine primersrnwhich contain different simple sequence repeat (SSR) were used and tested for PCRrnamplifications. A total of one hundred thirty seven bands were detected. The number of bands perrnISSR markers ranges from ten to twenty one with an average of 15.2. These were then used tornestimate the genetic diversity. Out of the total bands produced, 61(44.53%) were polymorphicrnand the number of polymorphic bands per ISSR markers ranges from one (1) to nineteen (19),rnwith an averages of 6.77. The similarities between individual genotypes were estimated usingrnUPGMA and NJ analysis. The populations were found to be clustered on the basis of theirrnrespective origin. The UPGMA cluster analysis showed that the four populations form two majorrnclusters (undisturbed and semi-disturbed populations together) according to locations from whichrnthey were collected. The two major clusters further divided into two. Analysis of molecularrnvariance (AMOVA) indicated that population level genetic diversity was relatively high (56.8%).rnShannonâ€™s diversity index showed the same patterns and indicated that the within and betweenrnpopulations genetic diversity of Coffea arabica L. populations are significantly different. Arnconsiderable proportion (83.6 %) of the total genetic diversity was distributed within populationsrn(i.e., due to differences among individuals within the populations). 16.4% of the total geneticrndiversity was due to differences among populations. Such distributions of the total geneticrndiversity could be attributed to gene flow via insect pollinators, seed flow by wild animals, birdsrnand human. Generally, on the basis of samples of 137 bands in the four populations, ISSR wasrnable to reveal moderate to high levels of genetic diversity within and among wild coffeernpopulations of Harenna Forest of Bale Mountain.rnKey Words: Coffea arabica L, ISSR marker, Harenna, Intra-regional analysis, Ethiopia