To better understand the cocoa transcriptome and to provide a framework for future investigations on cocoa functional genomics, approximately 175 000 cocoa clones from 52 cDNA libraries were sequenced. These libraries were constructed with RNA isolated from 13 genotypes (mainly from the two genotypes Scavina6 and ISC1) and from various tissues and organs (flowers, seeds, cherels, pod, shoot, root or embryos) under various conditions (fermentation, abiotic and biotic stresses). Suppression subtractive hybridisation (SSH) libraries were also produced under various plant pathogen interactions and from flowers pollinated by self compatible or incompatible pollen. From these cDNA libraries, 149 650 good quality ESTs were generated and analyzed using our "in house" bioinformatics pipeline. The assembly process produced 13837 contigs and 66746 singletons that represent 80583 different potential transcripts. These unigenes were assigned with BLASTX and BLASTN similarities, Gene Ontology annotation and protein domains. A comparison with public ESTs cocoa sequences already already available in public domain indicates that 80% of the unigenes may not have been described in public databases. (Texte intégral)