Random amplified polymorphic DNA (RAPD) analysis was used to assess the level of genetic diversity in an endangered plant Cerastiumfischerianum var. molle and the widespread conspecific C. fischerianum var. fischerianum. At both the variety and the population level, C. fischerianum var. molle had a lower level of RAPD variation than var. fischerianum. Analysis of molecular variance ( AMOVA) showed that most of the genetic diversity exists among populations for both varieties. Genetic differentiation among populations probably resulted from the highly selfing habits of both varieties. To conserve C. fischerianum var. molle genetically, preservation of only a part of the population is insufficient.