Fungi are masters of evolutionary adaptation, which have led to their enormous diversification and utilization as chemical factories of many potent secondary metabolites. Indeterminate growth and the capacity to produce distinct cell types are important sources of variation in fungal development. However, it remains largely unknown how natural selection on the genome drives adaptation of cellular morphogenesis. In many obligate mutualistic interactions the strong, but often narrow, selection pressure for a specific form or function provides an ideal framework for studying the genomic basis for fungal development. Our research identifies the key genetic adaptations of symbiotic fungi cultivated by fungus-growing ants to better understand the underlying evolutionary forces shaping fungal morphogenesis. A sub-group of these fungi form a distinct morphological adaptation to the symbiosis, i.e. inflated hyphal tips, called gongylidia. These structures are preferentially eaten by the cultivating ants and serve both as nutrition and as a source of fungal enzymes. These enzymes are important for efficient degradation of the plant substrate the ants use as substrate for cultivating the fungus garden. Using transcriptome sequencing and expressional profiling (RNA-seq) we identify and compare signatures of structural and expressional genetic adaptation in the evolution of these unique fungal structures.