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Theobroma cacao, a native tree from the Amazon Basin, produces the principal commodity for preparing chocolate. In Latin America, cacao production is threatened by biotic and abiotic conditions that limit the survival of this crop. Endophytic bacteria are reported to support plant health by growth-promoting abilities, suppression of pathogens and pests, and detoxifying environmental contaminants. As part of a larger study on the microbiome of cacao lead by the INDICASAT-STRI (Panama), the global objective of this study is to characterize the bacterial microbiota-associated with cacao pods of two cacao varieties grown under field conditions in Panama (CATONGO and CATIE-R6) and also those associated with Peruvian seeds from the cacao variety CCN-51. Culture-dependent and independent methods were applied to isolate and characterize bacteria from seeds (Panama and Peru) and from three layers of the …