The recalcitrance of Theobroma cacao L. to somatic embryogenesis, due to non-adapted physiological and metabolical responses to environmental stress, limits its propagation. The present work aims to ameliorate somatic embryogenesis in T. cacao throughout a physiological approach. For this purpose, the influence of the position of flowers buds used as explants was evaluated. Flowers buds were collected from different parts of the tree: orthotropic main stem (OS), primary plagiotropic fan branch (FI) and secondary plagiotropic fan branch (FII). Evolution of some biochemical parameters such as phenolic compounds, soluble sugars, proteins contents and peroxidase activity was followed at different steps of somatic embryogenesis, considering the origin of the explants used. Results obtained show that callogenesis is induced on all explants independently of their origin, with an 80% average frequency. Embryogenesis frequencies were ca 2 fold higher in staminodes-derived calluses from FII and FI than OS. Meanwhile petals of FII do not differentiate embryos. Biochemical analysis shows that the content of phenol is low in calluses during somatic embryo establishment. Explants from FII present the lowest values (after 49 th days of culture). Sugars content decrease during callogenesis. When embryos are established the sugars content decrease in explants from OS. During the same period, proteins' and phenols contents increased in staminodes-derived calluses from all origin; while there was decrease in petals from FI and FII. Buds from fan branch are suitable for somatic embryogenesis process and this capacity correlate with peroxidase activity which decrease during embryos dedifferentiation phase. (Wood et al., 1985). It is a diploid (2n=20) and preferentially allogamy plant. The root system has a growth dimorphism characterized by an orthotropic development axis, the pivot and plagiotropic lateral ramifications and lateral roots. Cocoa trunk is characterized by a vertical harbor (orthotropic), a phyllotaxis 3/8; long-stalked leaves, axillary orthotropic buds, a defined growth, differentiation of three to five plagiotropic buds under the apex, at the time of the degeneracy of the terminal bud. Cauliflorous tree, inflorescences cymes biparous with reduced inter-node develop at the flowering areas called flower cushions. The flowers are hermaphroditic, with small sizes (diameters ranging from 0.5 to 1 cm), regular and composed of 5 sepals, 5 petals, 5 staminodes, a pistil and an ovary. Pollination is predominantly entomophilous although it can be done manually in the experimental fields. Flowering in cocoa is manifested by the production of a minimum of 50 000 flowers during the term with less than 5% of production pods (Lass, 1999). Cocoa trees demonstrate a high degree of segregation for many traits when propagated by seeds. For this reason, clonal propagation systems such as rooted cuttings and grafting have been applied for multiplication of elite varieties but a vast majority of cocoa plants in production were derived f...