Flooding in rainfed lowlands greatly impairs the mutualistic relationship between indigenous arbuscular mycorrhizal fungi (AMF) and rice. In flooded soils, root colonization by AMF is arrested, but some AMF genera, defined as the core AMF, remain present. However, the core AMF in rainfed lowlands and their symbiotic roles remain unknown. Here, we showed that Acaulospora fungi were the core AMF in rice seedling roots of the Sangyod Muang Phatthalung (SMP) landrace rice variety grown in non-flooded and flooded paddy soils. Subsequently, indigenous Acaulospora spores were propagated by trap cultures using maize as the host plants. Therefore, to clarify the roles of cultured Acaulospora spores in a symbiotic partnership, the model japonica rice variety Nipponbare was grown in sterile soil inoculated with Acaulospora spores, and recolonized with a native microbial filtrate from the organic rice paddy soil. Our data demonstrated that the inoculation of Acaulospora spores in well-drained soil under a nutrient-sufficient condition for six weeks enabled 70 percent of the rice roots to be colonized by the fungi, leading to higher phosphate (Pi) accumulation in the mycorrhizal roots. Unexpectedly, the growth of rice seedlings was significantly suppressed by inoculation while photosynthetic parameters such as fractions of incoming light energy and relative chlorophyll content were unaltered. In the soil, the Acaulospora fungi increased soil phosphorus (P) availability by enhancing the secretion of acid phosphatase in the mycorrhizal roots. The findings of this work elucidate the symbiotic roles of the dominant Acaulospora fungi from lowland rice paddies.