Scrophularia fatmae Kandemir & İlhan and Scrophularia erzincanica R.R. Mill (Scrophulariaceae) are endemic
species to Erzincan/ Turkiye. IUCN categories in S. erzincanica and S. fatmae are EN and CR. In the present
study, we investigated levels of genetic variation and genetic structure of three populations of S. erzincanica,
and two populations of S. fatmae in Erzincan using ISSR markers. For this aim, 10 primers amplified 116 total
bands, with 104 (89.6 %) being polymorphic, from five populations composed of 75 individuals. The UPGMA
cluster analysis demonstrated a significant correlation between genetic variations and geographic distances. The
distribution area and population size of S. fatmae, which has adapted to the alpine region, is smaller than S.
erzincanica. In addition, S. fatmae has a higher tendency to self-pollination. The number of effective pollinators
in S. erzincanica and S. fatmae is three and one, respectively. When we compare S. fatmae and S. erzincanica
species according to the results of the research, it is seen that genetic diversity is higher in S. erzincanica. The
genetic data obtained as a result of the present study may be used in the development of conservation strategies
for other rare and endangered plant species, in addition to S. erzincanica and S. fatmae species.