As an inevitable natural factor, magnetic field has an important influence on the growth and development of organisms. However, there are few reports about the effect of magnetic field on large fungus growth. The growth and gene expression of Flammulina filiformis mycelium were detected by rubidium magnet treatment. The results showed that magnetic field of rubidium magnet inhibited the growth of Flammulina filiformis mycelium, and the inhibition was strong when the magnetic induction intensity was over 0.003T. A gene encoding the magnetic receptor named as ff-magr and an iron transporter ff-fief of Flammulina filiformis were obtained by homology matching. Quantitative PCR results showed that the expression of ff-magr was significantly down-regulated at both N and S poles, and the magnetic fields at both N and S poles had no significant effect on the expression of ff-fief, indicating that the magnetic receptor protein was involved in the response process of the inhibition of magnetic field, and the magnetic receptor not merely regulated the growth and development of mycelia by regulating iron content. The molecular mechanism of magnetic field influencing the growth and development of fungi needs further study.