With the rapid development of molecular biology, the molecular biological technologies have been applied widely in the field of mycorrhizal research. In this paper, the research progress in the mycorrhizal molecular biology was reviewed, including DNA barcode and genomic sequencing of mycorrhizal fungi, gene expression during the formation of mycorrhia, relevant protein expression changes in the process of mycorrhizal symbiosis’ nutrient uptake, the response of mycorrhizal aquaporins and SOD to stress conditions, as well as the limiting factors for development of mycorrhizal molecular biology. We proposed that more attention should be paid on screening appropriate model plant and mutant for mycorrhizal research, optimizing invitro culture technology for AM fungi and increasing the application of high-throughput sequencing technology in the future research.