Abstract: A total of 48 953 Unigenes were obtained by transcriptome sequencing of flower buds of Tagetes erecata. MISA found 20 666 SSRs located in 13 849 unigenes with the frequency of 28.29% and a mean distance of 2.51 kb per one. Trinucleotide and tetranucleotide were major types with the percentages of 50.16% and 20.94%，respectively. ATG/ATG and AAAC/GTTT were most frequent motifs in trinucleotide and tetranucleotide repeats，accounting for 13.82% and 3.66%，respectively. Based on different dominant motifs types，36 primers were chosen randomly and verified with 20 different inbred lines of Tagetes erecta. The results showed that 30 primers were effective with a valid rate of 80.56%，and 13 primers showed polymorphism with He and PIC mean values of 0.275 and 0.608，respectively. These data indicated that the Unigenes generated from transcriptome sequencing can be used as an effective source to develop SSR markers，and the large quantities of SSR markers will provide reliable resources for analysis on genetic polymorphism and constructing genetic map in Tagetes erecta.

Key words: Tagetes erecta L., SSR, transcriptome