Technical Abstract: Data-mining for expressed sequence tags (ESTs) containing simple sequence repeats (SSRs) has been demonstrated as an alternative method to generate genetic markers. The advantages are two-fold: the cost of identifying and developing useful markers is greatly reduced, and a putative function may be assigned to the locus based upon the sequence homology. We investigated converting ESTs isolated from Theobroma cacao L. into useful genetic markers for fingerprinting individuals and integration into genetic linkage maps. ESTs submitted into GenBank as of May 2005 were converted into a set of 2336 unigenes. Two hundred ten unigenes were identified as containing 293 SSRs, with AG-rich repeats dominating all size ranges. Primers were designed to 44 SSR-containing unigenes, 30 primer pairs gave polymerase chain reaction (PCR) products of the expected size. Twenty-six primer pairs were polymorphic and 28 potential loci could be mapped in at least one segregating population, with two primer pairs amplifying an additional product. Two primer pairs mapped three novel loci in an existing linkage map of an F2 population segregating for resistance to witches¿ broom disease, and five primer pairs distinguished one off type individual among 65 trees representing 22 cultivars. The overall 60% success rate suggests that approximately 120 useful SSR-EST markers can be developed from the current T. cacao unigene set for genetic mapping and fingerprinting.