Plant-fungal symbioses are a common feature in nature. They vary from pathogenic interactions, where fungi subvert plant resources for their own use, to mutualistic associations, where both fungus and host benefit from the interaction. Although the ecological importance of plant-fungal symbioses has long been recognized and the biology of several key associations are now well studied, new technologies have the potential to allow fresh insight into the molecular basis of plant-fungal interactions. One such technique - high throughput RNA sequencing - has recently been used to explore the molecular basis of cross-species communications. Here, we give a brief overview of this emerging technology, and present a general guide for employing the methodology to dissect plant-fungal symbiosis.