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Rosa rugosa Thunb. is one of the dominant and important shrub species in estuary dunes and shingle beaches of northern China. However, its area of distribution, the number of populations, and the size of each population have decreased rapidly in the past two decades because of habitat degradation and loss. Random amplified polymorphic DNA markers were used to determine the genetic diversity of four remaining large natural populations of R. rugosa and to discuss an effective conservation strategy for this endangered species in China. High genetic variations were detected in R. rugosa populations in China. The mean percentage of polymorphic loci (P%) within four local populations was 57.99%, with the P% of the total population being 75.30%. Mean Shannons information index (H_0) was 0.2826, whereas total H_0 was 0.3513. The genetic differentiation among populations was 0.1878, which indicates that most genetic diversity occurs within populations. Population Tumenjiang (TMJ) showed the highest genetic diversity (P% = 66.27%; H_0 = 0.3117) and contained two exclusive bands. Population Changshandao (CSD) showed higher genetic diversity (P% = 59.04%; H_0 = 0.3065). Populations TMJ and CSD contained 95.33% and 99.33%, respectively, of loci with moderate to high frequency (P>0.05) of the total population. These results indicate that populations TMJ and CSD should be given priority for in situ conservation and regarded as seed or propagule sources for ex situ conservation. The results of the present study also suggest that R. rugosa in China has become endangered as a result of human actions rather than genetic depression of populations; thus, human interference should be absolutely forbidden in R. rugosa habitats.