This research was performed simultaneously in the greenhouse and in the laboratory with the aim of agronomic and molecular characterization of four genotypes of Solanum betaceum Cav. tolerant to Colletotrichum acutatum of Patate area. Further to determine the phenotypic characteristics and genetic variability will allow segregating from productive to non productive plants. 40 agronomic descriptors were used to characterize four strains of the tree tomato from different locations like Leitillo, Los Andes and El Triunfo of Patate region. The result of the Ward hierarchical clustering revealed the existence of four genetic groups and among them plant with the code 138L2S1 was found to be a possible promising material with desirable characteristics: fruit size, earliness, production and tolerance to pests and diseases. In the laboratory phase or molecular characterization of four strains of tree tomato a molecular technique called Random Amplification of Polymorphic DNA (RAPD) was used, with the coefficient of Jaccard's similarity matrix for different genotypes was calculated and determined genetic variability through dendrogram analysis.