Transferability of five nuclear microsatellite markers (Jc-16, Jc-31, Jc-32, Jc-35 and Jc-37) that were originally developed for J. communis was tested to J. procera. Jc-31 & Jc-37 showed successful amplifications and polymorphism in J. procera. Jc-35 which had been reported as polymorphic in J. communis was monomorphic in J. procera while the primer pair for Jc-32 failed to record any amplification. The remaining one primer pair (Jc-16) showed double loci ampli-fication in both J. procera and the control J. communis suggesting further examination of the primer pair and its binding sites. Genetic variation of six Ethiopian J. procera populations: Chilimo, Goba, Menagesha-Suba, Wef-Washa, Yabelo and Ziquala was assessed based on the two polymorphic loci (Jc-31 & Jc-37) in 20 - 24 individuals of each population. From these two loci, a total of 41 alleles could be retrieved. Two populations that are located south east of the Great Rift Valley together harboured 75% of private alleles signifying their deviant geo-ecological zones and suggesting special consideration for conservation. Chilimo, which is at the western margin of Juniper habitat in Ethiopian central highlands scored the highest fixation (F_IS = 0.584) entailing lower immigrant genes and hence higher inbreeding. The AMOVA revealed that 97% of the variation resided within the population while still among population variation was significant (p < 0.05).