Abstract: 7087 EST of Chrysanthemum morifolium were assembled in order to provide molecular markers, and 275 contigs were obtained. There were 50 microsatellites (SSRs) were detected and averagely there was one SSR locus detected from 2854.3 bp of contigs. Trinucleotide repeats were the most abundant repeats(50.00%) among these SSR types. As for the composition of microsatellites, AC, AG repeats were the richest motif in dinucleotide repeats, and CAT, CCA repeats were the most frequent motifs in trinucleotide repeats, whereas (TTTN)n and (ATTTN)n repeats were dominant in tetra- and penta-nucleotide repeats, respectively. All the dominant repeat motifs for different type of SSRs were rich in A and T alkali bases. In EST of C. morifolium, microsatellites longer than 20bp accounted for about 2.00% of the detected SSRs. 428 pairs of primers were designed using Primer 5.0 and Oligo 6.0 according to these EST sequences containing SSR. 28 pairs of primers were randomly selected for PCR test with genomic DNA of Huangshan variety of Chrysanthemum morifolium, and 27 primer pairs succeeded in amplification, with successful ratio of 96.4%.