Swertia abyssinica (Hochst.) S. lugardae (Bullock) and S. pumila (Hochst.)rn(Gentianaceae) are closely related taxa occurring in the high mountains of North EastrnAfrica. Amplified Fragment Length Polymorphism (AFLP) markers were used to assessrnthe genetic variation between the higher and the lower altitude populations of the taxarnwithin and between different mountain regions. In a principal coordinate analysisrn(PCoA), the resulted grouping of accessions of the first two taxa corresponds with theirrngeographical locations rather than taxonomic classifications while S. pumila was far andrndistinct. Such groupings were inconsistent with previous study based on morphology.rnThe PCoA result was supported by the AMOVA with higher variations among mountainsrn(21.4 %) than variations within mountain among taxa (14.5 %). The considerablernreduction in variation among taxa (7.03 %) in the AMOVA excluding S. pumila and itsrndistinct position in the PCoA implies S. pumila as a different taxon. The evolutionaryrndistance tree based on AFLP characters supported the results from AMOVA and PCoA.rnThese results are in contradiction with the acceptance of three distinct species, but ratherrnsuggest as two distinct species. Thus the results suggest clinal morphological differencesrnbetween the two, S. abyssinica and S. lugardae. Thus it is likely that the clinal variation isrncaused by primary cline than hybridization. Although there was non - significantrnvariation between altitudes and weak correlation between them, it is difficult to concludernfor the absence of genetic base for the clinal morphological variation.rnKey words: Swertia, ecoclinal evolution, genetic diversity, glacial refugia, AFLP