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Leaf rust, which is caused by the fungus Hemileia vastatrix, is a devastating disease that affects coffee plants (Coffea arabica L).In this study, simple sequence repeat identification tool was used to screen SSRs in coffee leaf rust transcriptome.A total of 1292 SSRs were found in coffee leaf rust 9234 transcripts.Of the 1292 SSRs, the most abundant SSR is the tri-nucleotide type, with the SSR numbers being 459, followed by the di-and hexa-nucleotide ones, with 321 and 214 SSR numbers, accounting for 35.5%, 24.8% and 16.6%, respectively.Among the di-nucleotide repeats, AT/AT was the most motifs and accounted for 49.8%.However, ATC/ATG and AAG/CTT were both the most frequent motif among the tri-nucleotide repeats, accounting for 23.5% and 23.3%, respectively.Furthermore, the polymorphism of SSRs was assessed by filter out in the length of lower than 22bp SSR, and 223 potentially polymorphism SSRs were identified.Therefore, these results are useful to analyze genetic viaration, diversity,and evolution of coffee leaf rust pathogen.