Cacao (Theobroma cacao L.) is one of the main tropical crops worldwide. It is cultivated primarily to provide cacao liquor, butter, and powder for the chocolate industry, essentially due to its flavour properties. Unfortunately, destructive and newly encountered diseases have frequently been the major factors that limit cacao production in nearly all producing countries. The primary challenge is to develop improved cacao tree cultivars with durable and sustainable resistance to these diseases that at the same time have high bean quality for chocolate production. To achieve this goal, the use of functional genomics can be a key step to speed the development of such cultivars. During the last 10 years various functional genomics and some proteomic projects have been initiated, including expressed sequence tag and BAC libraries construction, cacao genome sequencing, expression studies of cacao tissues challenged with the main pathogens (Moniliophthora perniciosa, Phytophthora spp.) or subjected to other stress conditions (e.g. drought), and expression studies related to cacao quality flavour. Various others tools such as cacao in vitro culture, plant transformation or bioinformatics were developed to attend the necessity of cacao studies. Functional genomics research associated with genetics (molecular markers, maps and QTLs) will help to select new cacao varieties with agronomic characteristics demanded by farmers.