Species of the genus Agave are distributed originally in the tropical and subtropical areas of the American continent with about 200 taxa and 136 species, and its center of origin is probably limited to México. These kind of plants usually grow and live in extreme environmental conditions such as heat and drought where their CAM pathway for fixing CO allow them to survive in conditions where other plants cannot survive. Although this kind of plants resist harsh environmental conditions, climate change is imposing stronger kinds of stress that diminish their productive potential and in some cases are cause of death. Because of this, genetic improvement becomes a need of fundamental importance in this kind of species. Despite their economic importance, Agave species have received scarce attention with regard to its genetic improvement, probably due to their unique botanical features such as plant architecture, spines, long life span, and monocarpy, among others, which make hybridization a difficult task for the intra- and interspecific gene transfer and creation of genetic variability among many other breeding techniques.The protocol here presented is a combination of a novel hybridization technique and biotechnological tools, and allows the use of several procedures for the genetic improvement of agaves such as pollen selection, clonal selection, and somatic cell selection, among others, since the rescued embryos can be used for micropropagation, for phenotype/genotype selection or the production of cell lineages for diverse genetic improvement purposes.