Arbuscular mycorrhizal symbiosis is formed between the roots of over 80 % of all terrestrial plant species and Zygomycete fungi of the order Glomales. The beneficial effects of this symbiosis occur as a result of a complex molecular dialogue between the two symbiotic partners. Identifying the mole- cules involved in this dialogue is a prerequisite for a better understanding of the symbiosis. Although there is evidence for an interplay of signaling-recognition events at different stages during plant-fungal interactions in arbuscular mycorrhiza, the nature of signaling molecules and signal perception/trans- duction processes are still not known. To unlock the potential of arbuscular mycorrhiza for sustainable agriculture, we must identify the key molecular players. A number of methods are available for those researchers considering the addition of molecular analyses of arbuscular fungi to their research pro- jects and weighing the various approaches they might take. Increasingly powerful molecular methods for analyzing arbuscular communities make this area of research available to a much wider range of researchers.