Abstract: In this paper, the aims were to study on soil fungal genetic diversity variation characteristics during Salvia Miltiorrhiza Bge. cropping rotation period in Zhongjiang county of Sichuan province. Soil microbial DNA was saparated and extracted; then specific DNA fragments of fungi were amplified by PCR; the amplifying DNA fragments were saparated by DGGE；the strains were gained in GENBANK by the DNA sequencing. During the Salvia Miltiorrhiza Bge. cropping rotation period in Zhongjiang county，soil fungal community included: Termitaria sp. YAKU2，Agaricus bisporus，Cercozoan，Cordyceps，Geomyces destructans，Geomyces sp. P7，Cordyceps brongniartii，Penicillium sp. KCTC6774，uncultured Iodophanus clone S-54. Cluster analysis showed that the soil fungal community was similarity between fallow land 1year and this year；but it was obviously different from that of fallow land 3 years and 4 years. It was geared to the style of transition about fallow land 2 years. During the Salvia Miltiorrhiza Bge. cropping rotation period in Zhongjiang county，the soil fungal community and genetic diversity gradually recovered; the second year of fallow land was the key period of soil fungal community to restore; it was in agreement on our previous report conclusion.