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The variability of Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao (Theobroma cacao), was assessed based on measures of (i) mycelial growth rates (MGR), (ii) area of starch degradation (ASD) and (iii) aggressiveness towards susceptible and resistant clones. Ninety-six isolates were obtained from vegetative and flower cushion brooms from five resistant clones and one susceptible clone at two experimental sites at CEPEC, BA, Brazil. Seven isolates varying in the production of basidiospores, MGR and ASD were inoculated into six cacao clones being one susceptible, (SIC17) and five resistant (CCN10, Sca 6, TSH 1188, TSH 565, and TSH 516) to the disease. Disease incidence (SYMP) and severity (TNB, total number of brooms and DI, disease index) were assessed. Isolates obtained from TSH565, TSH516 and SIC17 VB were the most aggressive towards the cacao genotypes. MGR was not associated with aggressiveness, but ASD was significantly associated, at moderate levels, with disease incidence (r = 0.44; p = 0.018), TNB (r = 0.44; p = 0.018), and DI (r = 0.47; p = 0.012). Our results suggest that ASD is a promising biochemical marker to select for aggressiveness within M. perniciosa based on DI and TNB. On the other hand, MGR is a poor predictor of aggressiveness.