Theobroma cacao is very important in the economy of many tropical countries, especially in Ecuador. The development and production of Theobroma cacao have been limited by the attack of diseases, pests, and currently by the impact caused by the water deficit. The loss of water in the crop causes a low production of the plantations. In addition, when genetic diversity is scarce, the possible combinations of genes capable of conferring biological adaptation and, consequently, the capacity to adapt to environmental variations, are reduced. Therefore, a viable option is to identify genes capable of conferring adaptation to water deficit stress. The objective of this research was to characterize genes of Theobroma cacao in response to water deficit. The sequencing and characterization of genes related to water stress were achieved and, finally, the hybridization profile of the genes (ABA, ODC, DEH, and ABS) in response to Actin (ACT) was analyzed. The ABS gene hybridized 100 % with DNA from rootstock EET399 in roots and 80 % with DNA from graft T24 in leaves. The OCD gene hybridized 80 % with DNA from rootstock IMC 67 and 25 % with the T800 graft in leaves. The DEH gene hybridized below the normalizing gene (ACT) in both rootstock EET400 (10 %) in root DNA and graft T12 (5 %) in leaves. Finally, the ABA gene did not hybridize with the DNA of the CCN51 rootstock or with the graft (T801) in both roots and leaves, respectively. This research is key to understand some molecular mechanisms of T. cacao in response to water deficit and can be considered as a viable strategy to reduce crop agronomic losses under the current environmental scenario.