Abstract：Genetic diversity and differentiation of five natural populations of Carya cathayensis Sarg. were studied with the method of RAPD. Using 2010 bp selected random primers, 252 repeatable loci were detected, of which 66.7 % loci were polymorphic. According to the measurement of Shannon index, genetic diversity of Carya cathayensis was on relatively high level and genetic variation mainly distributed within Populations (60.32 %).Among 5 populations ,the genetic diversity level of Daoshi population was the highest （0.2800）, that of Linmu population was the lowest (0.1992) .The average genetic distance within populations