The continuous cropping of potato could result in the imbalance of soil microbial community structure，the aggravation of soil borne diseases and soil degradation，while crops rotation can alleviate these negative effects.In order to investigate the effects of continuous cropping and rotation on soil microbial community structure of three potato varieties (HeZuo88，LiShu6，QingShu9)in Yunnan，the rhizosphere soil fungal community structure was studied by high-throughput sequencing technology.The results showed that continuous cropping increased the abundance of Mortierellomycota， unclassified_Ascomycota and Mortierella by 4.30%， 113.82% and 1.60% in Hezuo 88 soil.The rotation of Hezuo 88(HZ88)-Tartary buckwheat(KQ) and KQ-H88 decreased by 31.06% and 45.01%， 87.04% and 7.14%， 40.43% and 45.53%， respectively.Continuous cropping increased Ascomycota abundance by 7.57% in Lishu 6， but rotation of Lishu 6(LS6H)-KQ and KQ-LS6H decreased by 50.72% and 1.22%， respectively.Continuous cropping increased the abundance of Basidiomycota and Rozellomycota by 11.35% and 50.79% in Qingshu 9.The rotation of Qingshu 9 (QS9H)-KQ and KQ-QS9H decreased by 22.12% and 52.59%， 74.22% and 22.22%， respectively.In addition， compared with HZ88-HZ88， LS6H-LS6H， QS9H-QS9H， the abundance of Ascomycota in H88-KQ and KQ-H88， LS6H-KQ and KQ-LS6H， QS9H-KQ and KQ-QS9H soil decreased significantly by 46.07% and 9.11%， 53.59% and 18.13%， 9.44% and -12.87%，respectively.Plectosphaerella abundance decreased significantly by 94.27% and 17.41%， 86.07% and 45.17%， 63.11% and -427.04%，respectively.The abundance of unclassified_Ascomycota decreased significantly by 94.64% and 74.97%， 97.34% and 22.97%， 85.73% and -32.56%，respectively.The change of soil fungal community structure may be one of the important reasons for potato continuous cropping obstacles in Yunnan，and rotation can effectively alleviate them.