Resistance and defence gene analogs (RGA and DGA) have been isolated in cocoa using a PCR-based approach. Among 36 cocoa DNA fragments homologous to known resistance or defence genes, 16 corresponding to unique RFLP profiles could he mapped. One cluster of DGA and three clusters of RGA have been identified in the cocoa genome. One cluster corresponded to 2 PR2 like sequences, two clusters corresponded to genes encoding cytoplasmic receptor-like protein containing a nucleotide binding site (NBS). The third RGA cluster gathered four analogs to the tomato Pto gene and one analog to the LRK10 wheat rust resistance gene, corresponding to genes which contain a serine threonine kinase domain (STK). This last cluster colocalised with 4 QTLs of resistance to Phytophthora identified in previous QTL mapping studies. A BAC library was constructed from the Scavina 6 resistant genotype and used to begin physical mapping of the chromosome regions containing these RGA/DGA clusters.