Abstract: The present paper aimed to investigate the diversity of eukaryotic structure in rhizosphere soil of 4 deciduous fruit trees. The diversity of eukaryotic structure in the rhizosphere soil of pomegranate, peach, cherry and ginkgo was sequenced and compared by high-throughput sequencing technique. The results showed that 2368 OTUs were obtained by sequencing. The Shannon index of ginkgo sample was higher and the Simpson index was lower, which indicated that the eukaryotic structure diversity of ginkgo sample was high. The chaol index and ACE index of ginkgo sample were higher than those in the other three samples, which indicated that the richness of eukaryotic community of ginkgo sample was higher. There were four dominant fungal genera in the fungal community of pomegranate sample at the genus level, which mainly included 18.68% of Chaetomium and 6.77% of Fusarium. There were five dominant fungal genera in the fungal community of peach sample at the genus level, which mainly included Fusarium（8.87%） and Chaetomium（7.00%）. There were six dominant fungal genera in the fungal community of cherry sample at the genus level, which mainly included Chaetomium（22.66%）, Fusarium（15.91%） and Mortierella（11.16%）. There were seven dominant fungal genera in the fungal community of ginkgo sample at the genus level, which mainly included Chaetomium（9.08%） and Parastagonospora（5.83%）. The dominant groups of the four fruit samples were fungi, and the fungal communities in rhizosphere soil of different fruit samples were different.

Key words: deciduous fruit trees, high-throughput sequencing, diversity analysis