SSR (simple sequence repeats) markers derived from ESTs (expressed sequence tags), commonly called EST-SSRs or genic SSRs provide useful genetic markers for crop improvement. These are easy and economical to develop as by-products of large-scale EST resources that have become available as part of the functional genomic studies in many plant species. Here, we describe for the first time, nine genic-SSRs of coffee that are developed from the microsatellite containing ESTs from a cDNA library of moisture-stressed leaves of coffee variety, ‘CxR’ (a commercial interspecific hybrid between Coffea congensis and Coffea canephora). The markers show considerable allelic diversity with PIC values up to 0.70 and 0.75 for Coffea arabica and Coffea canephora, respectively, and robust cross-species amplification in 16 other related taxa of coffee. The validation studies thus demonstrate the potential utility of the EST-SSRs for genetic analysis of coffee germplasm.