Soil fungi play a pivotal role in health and stability of rhizosphere ecosystem. The genus Sonneratia were a pioneer group of dominant mangrove plant species. In this study, the rhizosphere fungal diversity and composition of six species of Sonneratia mangrove were investigated by Illumina high-throughput sequencing method with the internal transcribed spacer-1 region, the influencing factors were also discussed combining the physical and chemical properties of soil. The results showed that the rhizosphere fungi communities distributed into 7 phyla, 96 families, and 155 genera were dominated by Ascomycota members with relative abundances more than 27%. No significant differences were observed among the six mangroves species at phylum level, except for the relative abundances of Basidiomycota. Significant differences were observed at the genus level, such as a higher relative abundance of Aspergillus was 29% in S. ovota, but the abundance was only 3% in the S.×hainanensis. Some special members of fungi were enriched to representative populations in different mangrove species, such as the relative abundance of Malassezia and Trichorotium was 9.31% and 10.05%, respectively, in S. apetala, while in the mangrove S.×hainanensis, the representative members were Talaromyces (19.61%) and Acremonium (13.58%). Comparing the Simpson and Shannon index of the six mangrove plants, the index was the highest in S.×gulngai, the lowest was in S.ovota. These results indicated that plant genotype could affect the composition of rhizosphere fungi. Analysis of soil physical and chemical properties found that the soil available potassium content was significantly positively correlated with the relative abundances of Basidiomycota, total phosphorus content was negatively correlated with the abundance of Ascomycota. The rhizosphere core fungal diversity and analysis of six Sonneratia species of the genus mangrove showed that the dominant fungal group Aspergillus and some low abundance fungal groups, which participated in the carbon cycle by degrading organic matter, played an important role in the stabilization of the rhizosphere soil ecosystem. In short, the rhizosphere fungal communities of the Sonneratia mangroves were highly diverse and rich, and some representative fungal species colonized in the rhizosphere of different mangrove plants. These fungi can form a good symbiotic relationship with the Sonneratia mangroves, providing nutrients for the mangrove ecosystem and increasing the growth rate of the mangrove forest. In this study, the community diversity of rhizosphere fungi was investigated in the Sonneratia mangrove, which provided some essential data on effective protection, reasonable utilization of Sonneratia mangrove resource, and population restoration.