This review summarizes the most recent results obtained using molecular biological techniques in the understanding of the arbuscular mycorrhizal symbiosis. On the plant side, cDNA libraries have been established from mycorrhizal RNA using several techniques, such as suppressive subtractive hybridization, and a large number of clones are being sequenced to obtain expressed sequence tags (ESTs). These ESTs can be transferred to solid supports (arrays) and hybridized with cDNA from different sources to obtain RNA accumulation profiles of genes expressed during the mycorrhizal symbiosis. On the fungal side, EST libraries are also being established, both using direct cloning and suppressive subtractive hybridization techniques. For both partners, the next steps are the detailed analysis of some relevant genes concerned with regulation and function, as well as the study of their role in the symbiosis. At the end of this review, we discuss how results about gene expression and functioning from molecular analyses can help in understanding the ecology of the symbiosis and the way in which it can be further exploited for application in plant production systems.