The endophytic root colonising basidiomycete fungus, Piriformospora indica isolated from the Indian Thar desert, belongs to Sebacinales. The fungus interacts with the roots of many plant species including Arabidopsis thaliana and promotes growth, development and seed production and also confers resistance to various biotic and abiotic stress. The fungus can be cultivated axenically on synthetic or complex media without a host. The endophytic interaction of P. indica with the model plant A. thaliana helps to understand the molecular and physiological basis of beneficial interactions between two symbionts. To study this interaction, both partners should be grown together in harmony. Here we describe detailed and optimized protocols for in vitro and in vivo co-cultivation of P. indica and A. thaliana, which can also be used for other plant species.