To effectively conserve sour orange(Citrus aurantium L.) germplasm on two islands at the estuary of the Yangtze River in China,we estimated genetic variation and relationships of the known parental trees and their proposed descendents(young trees) using the fingerprints of random amplified polymorphic DNA(RAPD).Results based on RAPD analyses showed considerable genetic diversity in the parental populations(He = 0.202).The overall populations including the parental and young trees showed slightly higher genetic diversity(He = 0.298) than the parents,with about 10% variation between populations.An unweighted pair group method with arithmetic mean analysis dendrogram based on cluster analysis of the Jaccard similarity among individuals demonstrated a more complicated relationship of the parental and young trees from the two islands,although the young trees showed a clear association with parental trees.This indicates a significant contribution of parental trees in establishing the sour orange populations on the two islands.According to farmers’ knowledge,conservation of only one or two parental trees would be sufficient because they believed that the whole populations were generated from a single mother tree.However,this study suggests that preserving most parental trees and some selected young trees with distant genetic relationships should be an effective conservation strategy for sour orange germplasm on the two islands. We effectively genetic and relationships of the known parental trees and their proposed descendents (young trees) using the fingerprints of random amplified Polymorphic DNA (RAPD). Results based on RAPD analyzes showed extensive genetic diversity in the parental populations (He = 0.202). The overall profiles include the parental and young trees showed slightly higher genetic diversity (He = 0.298) than the parents, with about 10% variation between populations. An unweighted pair group method with arithmetic mean analysis dendrogram based on cluster analysis of the Jaccard similarity among individuals demonstrated a more complicated relationship of the parental and young trees from the two islands, although the young trees showed a clear association with parental trees. This indicates a significant contribution of parental trees in establishing the sour or ange populations on the two islands. According to farmers’ knowledge, conservation of only one or two parental trees would be sufficient because they believed that the whole population were generated from a single mother tree. However, this study suggests that preserving most parental trees and some selected young trees with distant genetic relationships should be an effective conservation strategy for sour orange germplasm on the two islands.