Mexico is the world's largest producer, exporter, and consumer of avocado fruit, with the state of Michoacán being the main producer in the country. Plants of the native Mexican avocado (Persea americana var. drymifolia) are used in Mexico and other countries as a rootstock for the main commercial cultivars (for example, 'Hass'). However, despite the importance for fruit production of this cultivar of avocado, little is known about its genetic background. We generated and analyzed ESTs libraries from different fruit structures of the "native Mexican" avocado. We found that the fruit transcriptome is dominated by the expression of genes involved in stress responses and innate immunity. It showed antimicrobial activity in the protein product of defensin and, an innate immunity isolated gene. These genes are assumed to function against avocado postharvest pathogens. Our finding could be relevant for developing biotechnology strategies to protect fruits and other horticultural products during the postharvest period.