Jatropha curcas (Jatropha) is an oil-producing plant with multiple uses, especially the great potential of energy application. Germplasm collection and evaluation are essential for breeding new cultivars with high yield, good quality and wide adaptation. In the present study, we investigated genetic diversity of Chinese Jatropha germplasm by using ISSR markers. A set of 224 accessions including 219 from all the adaptation areas in China and five from Myanmar was adopted. Out of 100 UBC ISSR primers, 15 that had good reproducibility were selected to genotype the population. Among the 169 amplified bands, 127 (75.15%) were polymorphic which meant that Chinese Jatropha had high genetic diversity. Population genetics analysis showed that average Nei's gene diversity (He) was 0.19, and average Shannon Information Index (I) was 0.292, indicating a relatively high genetic variation in the collections. The dendrogram based on Nei's genetic distance showed that distinct genetic differentiation occurred in Chinese Jatropha, most of the mainland accessions were clustered into a sub-group (Ia), and accessions from Hainan Island and its neighboring Guangdong province were generally clustered into another sub-group (Ib). A core germplasm collection was established by SCR strategy. This core collection consisted of 46 accessions that accounted 20.54% of the initial collection, and maintained over 90% of observed alleles, polymorphic loci and polymorphism rate. Slight correlation of oil content variation and genetic diversity was observed. Tropical populations are the most important genetic resources and crosses between this tropics and the mainland are recommended for genetic improvement of Jatropha in China. (C) 2010 Elsevier Ltd. All rights reserved.