| Sea buckthorn (Hippophae rhamnoides) is well adapted to arid regions and is utilized for multiple purposes in China. To provide a population-level genetic profile for further investigation and conservation of genetic diversity of sea buckthorn, 380 individuals of nineteen natural populations of sea buckthorn in northeastern, northwestern and southeastern China were analyzed to detect genetic variation among and within populations by use of ISSR (Inter-simple sequence repeats) markers. Using 8 primers, 288 polymorphic loci were observed, ranging in size from 250bp to 2500bp. Based on Shannon,s index and Nei,s genetic diversity , the genetic diversity detected in the natural populations of Hippophae rhamnoides ssp. yunnanensis, ssp. sinensis and ssp. gyantsensis was not significantly different. The coefficient of gene differentiation (Gst ) of 7 yunnanensis populations is 0.2790, and it is 0.4096 for 11 sinensis populations. This suggests that the genetic variation among yunnanensis populations and sinensis populations are 27.90% and 40.96% respectively, which indicated that the genetic structures are different for sspecies. The coefficient of gene differentiation (Gst=0.4320) showed that 56.80% of the total molecular variance of 19 populations of Hippophae rhamnoides was existed within populations. This result is important to the conservation of sea buckthorn genetic resources. Especially, in a situation of limited collection and management capacity in germplasm conservation, the recommendation is to collect more individuals in each population but less populations to preserve more individuals than populations according to this result. The UPGMA cluster analysis (CA) showed that there was no distinct genetic differentiation between populations from different area. No significant correlation between genetic and geographic distances of the populations was found using ISSR markers.The chemical composition of leaves from 14 populations of Hippophae rhamnoides ssp. yunnanensis and ssp. sinensis was analyzed by GC-MS. Of the 45 compounds represented, 40 compounds were identified. The principal componentsanalysis (PCA) and cluster analysis were performed for investigating the inter-population variability of the chemical composition. Our results indicated that the distribution of tetracosane, eicosanol and hexadecanoic acid have significant value for distinguishing H. rhamnoides ssp. yunnanensis and H. rhamnoides ssp. sinensis from each other. Tetracosane is the major constituent present in all samples, with its highest percentage found in Population SL3 and Population SL7 (40.96% and 39.42% respectively). However, in populations of H. rhamnoides ssp. sinensis, the content of tetracosane is obviously higher than that in populations of H. rhamnoides ssp. yunnanensis (p<0.01), and the same trend is found on the content of eicosanol. Furthermore, hexadecanoic acid is the major constituent of the chemical composition of H. rhamnoides ssp. yunanensis populations, but was not detected in H. rhamnoides ssp. sinensis. Accordingly, two main chemotypes, one hexadecanoic acid and eicosanol rich including all seven populations of H. rhamnoides ssp. yunnanensis samples, and the other tetracosane rich including all seven H. rhamnoides ssp. sinensis samples, were well differentiated. The PCA and CA of the chemical composition revealed that the chemical composition of leaves is associated with geographical distribution. The three-dimensional plot of the principal component scores (total 98.3% information in the first three components) showed the relationship between chemical composition of leaves and geographical distribution clearly.The mantel test showed that there was no significant correlation between the two distance matrices based on the genetic distance matrix and the chemical components matrix (r = 0.5464, Prob. Random Z < obs. Z: p = 1.0000). But we found, by genetic distance, the two subspecies were distinguished clearly, so did the chemical distance. So, we expected that there should be a congruence of inter-population rel...
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