Greenhouse-grown susceptible 20-d-old seedlings of Theobroma cacao genotypes Catongo and tolerant genotype SCA6xCatongo were inoculated with a mixture of isolates of Crinipellis perniciosa, the causal agent of witches' broom. The characteristics of chlorophyll a fluorescence emission were monitored during leaf ontogeny using a portable system PAM-2000. In both inoculated and non-inoculated genotypes, significant differences were found for the effective quantum yield values of photosystem (PS) 2 (ΔF/Fm') at the B (7 to 14-d-old), D (21 to 30-d-old), and E (>30-d-old) stages of leaf development, and in quantum yield of the non-cyclic photosynthetic electron transport between PS2 and PS1 [qp(Fv/Fm)] and quencher efficiency [(Fm-Ft)/F0] at the B, C (15 to 20-d-old) and D stages. Intergenotypic differences were found only for the [qp(Fv/Fm)] and [(Fm-Ft)/F0] values at the E stage, and for fluorescence quenching (Fm-Ft) at the B and E stages. Highly significant inter- and intragenotype relationships were found between the rate of photosynthetic electron transport to PS2 (Amax) and maximum fluorescence during actinic irradiation (Fm'). Also, each of the highly significant relationships between (Fm-Ft) and Amax, [(Fm-Ft)/F0] and ΔF/Fm', and between [(Fm-Ft)/F0] and Amax were represented by a general model, independent of treatments. Therefore, alterations in energy distribution in the radiant energy collector complex interior of PS2 and reduction in absorption of photosynthetically active radiation were observed in the infected plants, mainly in the hybrid at the C stage. Also, variations were found in the noncyclic photosynthetic electron transport at the B and C stages in the infected Catongo. and I. C. F. Santos, A.-A. F. de Almeida, R. R. Valle.