Centaurea nivea (Asteraceae) is endemic to Turkey and distributed only in the Eskişehir Province. It is under risk of extinction due to anthropogenic disturbance, so conservation strategies must be developed urgently. In this study, RAPD technique was used to estimate the level of genetic diversity of C. nivea. Twenty RAPD primers generated 234 bands, of which 215 were polymorphic (91.88%). A high level of genetic diversity was detected both at population (PPB = 72.90%, I = 0.3790, H_s = 0.2527) and at species level (PPB = 91.88%, I = 0.4510, H_t = 0.2963). A moderate level of genetic differentiation among populations was also revealed by Nei's gene diversity analysis (14.73%), Shannon's information measure (15.96%) and AMOVA (7.97%). Patterns of genetic variation among the populations of C. nivea may indicate that the closely located and fragmented populations of C. nivea were likely derived from a previously large population.