Random Amplified Polymorphic DNA (RAPD) markers were used to measure genetic diversity of Changium smyrnioides Wolff (Apiaceae), a genus endemic to eastern China and an endangered medicinal plant, collected from five populations along the Yangzi River. A total of 92 amplified bands were scored from the 13 RAPD primers, and a mean of 7.1 amplified bands per primer and 69%(64 bands) percentages of polymorphic bands (PPB) was found. The Shannon's index was used to partition genetic diversity. Genetic diversity estimates indicated that 51.2% of total diversity was among populations and 48.8% within populations. The species shows higher genetic diversity between populations than other endangered plants. In this study, the RAPD results of genetic diversity are similar to those of previous studies employing allozymes (58% among populations and 42% within populations). The RAPDs provide a useful tool for assessing genetic diversity of rare, endemic species and for resolving relationships among populations. The results show that the genetic diversity of this species is high, possibly allowing it to more easily adapt to environmental variations. A pattern of greater variation among rather than within populations was observed with both markers. This distributive pattern of genetic variation of C. smyrnioides populations provides important baseline data for conservation and collection strategies for this species. It is suggested that most of the populations should be sampled in ex-situation protection so as to retain as much genetic diversity as possible.