A detailed and curated map of molecular interactions taking place in the polyphenols (flavonoids) biosynthesis in Theobroma cacao L. is presented. The map was created using the software Cytoscape v.2.7 and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. The statistical parameters of the network were determined with CentiScape v.1.1 and MetaAnalyzer v.2.6.1. A preliminary theoretical map containing 1024 chemical species and 1099 chemical reactions was built, then a second map that was curated and annotated with the biological facts obtained from approximately 85 publications in T. cacao, with 653 chemical species
and 706 chemical reactions. Structural analysis of this interaction network revealed similitude with other biological networks. The study of complex networks opens the way for creating realistic computational models of flavonoid biosynthesis metabolic pathways in cacao.