Abstract: Eighteen EST-SSR primer pairs were used to amplify SSR fragments for 8 Sect. Rhysocayon samples，14 Sect. Cardiocaryon samples，28 Sect. Juglans samples in Juglans L. and 4 C. illinoinensis samples in Carya Nutt. The 18 pairs of EST-SSR primers generated a total of 110 alleles. The number of alleles per locus ranged from 3 to 10，and averaged 6.1. The observed heterozygosity（Ho）of 18 EST-SSR loci ranged from 0.057 to 0.574，and averaged 0.323. The value of allelic polymorphism information content（PIC）ranged from 0.3723 to 0.8795，and averaged 0.6890. The average percentage of available loci amplified in C. illinoinensis，Sect. Rhysocayon，Sect. Cardiocaryon，J. regia and J. sigillata samples are 87.5%，96.3%，98.8%，100% and 99.8%，respectively. It showed that the EST-SSR had good transferability among species in Juglans L. and Carya Nutt. In the dendrogram，the samples clustered clearly among species or sect. in Juglans L. and Carya Nutt，and the result accorded with the conventional taxonomy. In J. regia，the samples could be clustered into 3 ecological types，namely Xinjiang walnut，Huabei walnut and Tibet walnut. The walnut samples from Shaanxi clustered together with those from Beijing，Shandong and Henan. It indicated that Shaanxi walnuts and Huabei walnuts probably belonged to the same ecological type. In J. sigillata，‘Jinshajiang 1’，‘Jinshajiang 2’and‘Yongping Tie-walnut 1’clustered together as the group of J. sigillata. But the other two samples of J. sigillata，named‘Santai’and ‘Lijiang tie-walnut 1’，clustered together with‘Lijiang walnut 1’and Tibet walnuts. It indicated that，‘Lijiang walnut 1’should belong to Tibet walnut ecological type，and some samples of J. sigillata have closely relationship with Tibet walnuts. J. sigillata and J. regia live together，which possibly lead to some offspring of J. sigillata coming from J. Sigillata × J. regia.

Key words: walnut, EST-SSR, Relatedness, ecologicaltype