Prickly pear (cactus fruit) is an important crop in Mexico, it helps to the establishment of Mexican antique civilization. As a ripening model, it has a unique character because include morphospecies with contrasting characteristics, making easier their interpretation. The main commercialization problems for prickly pear include the presence of seeds and spines (gloquids), it would be interesting to idenfied the genetic factors involve in their synthesis of these structures, through genetic expression in order to design some strategy for their control. In this study we have been used different molecular and bioinformatics strategies for the identification of the factors related to prickly pear development. In proteomics assays using three morphospecies with contrasting development and fruit ripening, it was possible to identified the minimal number of required peptides for fruit development and ripening delay, also were identified peptides associated to regulatory functions in transcendental metabolic functions. In the miRNA transcriptome, were identified 255 molecules associated to the fruit development and other important process, such as adaptation to extremal growth conditions, were cactus plants growth. Seven families of miRNAs were associated to fruit development and plant adaptation, and the pathway of miRNA participation was determined. The expression assays shown the effects of miRNAs on fruit development in prickly pear.