Introduction:

The objectives of the work were to characterize the morphological and genetic variability of traditional Cuban cacao to classify it in the traditional and genetic groups of the crop, To characterize morphologically and molecularly the species of Phytophthora, causing the black pod disease in Cuba.

Methods:

Traditional Cuban cacao was characterized with 33 qualitative morphological descriptors and DNA was amplified with the 15 cacao microsatellites standard for its genetic characterization. With the structure program, the population structure was determined and classified into the 10 genetic groups of cocoa. With these results, the plants were selected for the core collection by means of the algorithm of maximum genetic diversity. Phytophthora strains isolated from diseased fruits were studied, morphologically characterized under the microscope and DNA was extracted for phylogenetic analysis by amplifying β-tubulin, TEF1-α and ITS.

Results:

It was observed that Cuban plants have high morphological variability and low genetic variability. They were classified into seven genetic groups, but most constitute a mix between Criollo and Amelonado, which indicates that they belong to the traditional Trinitario group. Based on these results a core collection was selected. In addition, a group of Phytophthora strains isolated from diseased pods of Cuba were studied, combining morphological and molecular aspects to identify the species involved. Conclusions: Traditional Cuban cacao was classified as Trinitarian, with potential for genetic improvement, and the Phytophthora species that mainly affect cacao fruits are P. palmivora and P. tropicalis.

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