Arbuscular mycorrhiza (AM) formed between plant roots and fungi is one of the most widespread symbiotic associations in nature. To understand the molecular mechanisms of AM formation, we profiled 30 symbiosis-related genes expressed in Amorpha fruticosa roots colonized by Glomus mosseae and in non-mycorrhizal roots at different stages using differential-display RT-PCR (DDRT-PCR). The expressed genes were confirmed by reverse Northern blotting. Eleven fragments were sequenced and putatively identified by homologous alignment. Of the eleven AM-related genes, five were obtained at the early-stage of plant-fungus interaction and six at the later stage. Three expressed sequence tag (ESTs) sequences were found to originate from the fungi and eight from the host plant by use of PCR evaluation of gDNA of both plant and fungi. The target genes included an ATP-binding cassette sub-family transporter gene, a transposon-insertion display band, and a photosynthesis-related gene. The results provided information on the molecular mechanisms underlying the development of mycorrhizal symbiosis between woody plants and AM fungi.