Abstract: Chloroplast simple sequence repeat（cpSSR）and expressed sequence tag-simple sequence repeat（EST-SSR）markers were used to reveal Citrus and its related genera phylogenetic relationship and to clarify the genetic background of some unique citrus germplasms conservered in National Citrus Germplasm Repository（Chongqing）. Fifty and forty-four accessions were used for cpSSR and EST-SSR analysis respectively. Twenty-two pairs of cpSSR specific primers generated 146 bands with an average of 6.64 alleles per locus and an average Shannon’s information index of 0.32；Eighteen pairs of EST-SSR primers produced 240 bands with the mean of 13.3 alleles per locus，the mean polymorphic information content（PIC）was 0.73 and expected heterozygosity was 0.78. In addition, the genetic origin of some unique citrus accessions were also clearly clarified by cpSSR and EST-SSR analysis combining with the
morphological characteristics，meanwhile，it was showed that Ichang Papeda have close phylogenetic relationship with Mangshan Yeju and Yuan Ju.

Key words: Citrus, cpSSR, EST-SSR, genetic background