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Abstract Tropical tree communities are among the most diverse in the world. A small number of genera often disproportionately contribute to this diversity. How so many species from a single genus can co‐occur represents a major outstanding question in biology. Niche differences are likely to play a major role in promoting congeneric diversity, but the mechanisms of interest are often not well‐characterized by the set of functional traits generally measured by ecologists.To address this knowledge gap, we used a functional genomic approach to investigate the mechanisms of co‐occurrence in the hyper‐diverse genusFicus. Our study focused on over 800 genes related to drought and defence, providing detailed information on how these genes may contribute to the diversity ofFicusspecies.We find widespread and consistent evidence of the importance of defence gene dissimilarity in co‐occurring species, providing genetic support for what would be expected under the Janzen‐Connell mechanism. We also find that drought‐related gene sequence similarity is related toFicusco‐occurrence, indicating that similar responses to drought promote co‐occurrence.Synthesis. We provide the first detailed functional genomic evidence of how drought‐ and defence‐related genes simultaneously contribute to the local co‐occurrence in a hyper‐diverse genus. Our results demonstrate the potential of community transcriptomics to identify the drivers of species co‐occurrence in hyper‐diverse tropical tree genera.