Abstract Searching for new approaches to confer resistance to diseases in plants is one of the main objectives of the Cacao breeding program (CBP). Witches' broom (WB) and black pod rot (BPR) are important cacao diseases in Bahia, Brazil. This study aimed to evaluate the resistance in plants from 40 progenies of genetic crosses between elite clones to natural infection by high levels of Moniliophthora perniciosa and Phytophthora spp. WB and BPR infection assessments were conducted in the field, including evaluation of vegetative brooms (VB), cushion brooms (CB), and total brooms (TB), as well as the percentage of WB-diseased (FRUWB) and BPR-diseased (FRUBPR) fruits. Ten progenies showed resistance to infection in both the canopy and fruits. No significant differences between the progenies were detected for FRUBPR.