Abstract: The transcriptomes of Eucommia ulmoides ‘Huazhong 12’ young and mature leaves and ‘Huazhong 11’ mature leaves were sequenced. The transcriptome data was assembled and classified by function, and microsatellites characteristics from obtained Unigenes and analyzed. The Unigenes were assembly generated a total of 54 517 Unigenes with an average length of 806.90 bp. Among them, 25 993 Unigenes accounted for 47.68% were annotated by comparing the assembled Unigenes with the Nr, Swiss-Prot, KEGG, and COG protein databases. KEGG pathway analysis presented that 6 910 annotated Unigenes divided into 122 classes according to its function. Among them, the Unigenes of ascorbate and aldarate metabolism was 39, flavonoid biosynthesis was 38, carotenoid biosynthesis was 34. There were 17 010 complete SSR located in 54 517 Unigenes accounted for 96.28% of the total SSR. The complete SSR included 67 frequent motifs, and the highest repeat of complete SSR type was A/T(7 747), following by AG/CT(5 039), AT/AT(850). There were 13 SSR located in ascorbate and aldarate metabolism, flavonoid biosynthesis and carotenoid biosynthesis. Our study would provide the molecular basis for genetic diversity analysis, genetic map construction and red leaf molecular marker development of E.ulmoides.