Ceratocystis cacaofunesta is an ascomycete responsible for the lethal wilt disease of cacao (Theobroma cacao L.). Marker-assisted selection combined with conventional breeding is one powerful approach to improve cacao resistance to Ceratocystis wilt. In this study we screened a set of ESTs obtained from cacao elicited with C. cacaofunesta to identify EST-SSRs and test their efficacy for mapping. Among the 3,432 ESTs analysed, 384 contained SSRs and 428 EST-SSRs were identified, mainly dinucleotides (78.5 %), with four repeats (75.23 %), and preferentially AG/CT motif (25.47 %). Gene ontology function was assigned to the ESTs containing SSRs: 4.04 % belonged to "defense response" category, with 20.69 % of them to the sub-category "defense response to fungi". In relation to the ORF, the same quantity of EST-SSRs was observed in the 5? UTR, ORF and the 3? UTR (about 30 %). From the 428 EST-SSRs identified, 12 were polymorphic, revealing a total of 41 alleles. The number of alleles per locus ranged from 2 to 6, with an average of 3.41. Four EST-SSRs were mapped on the F2 Sca 6 × ICS 1 population segregating for Ceratocystis wilt, and were distributed on the 2, 3, 4 and 8 linkage groups. These markers will have potential applications in linkage mapping and will be valuable for the research community to improve the cacao breeding program.