Ammopiptanthus mongolicus is an endangered broadleaf leguminous plant found in the desert ecosystem of northwest China, and it is also an excellent sand fixation plant. Zygophyllum xanthoxylum, Tetraena mongolica, Nitraria Tangutorum and Artemisia desterorum are plants that associated with A. mongolicus. These plants undergo competition inhibition and cooperative evolution, and are ideal for improving desert areas and preventing desertification. Arbuscular mycorrhizal (AM) fungi can form symbioses with most terrestrial plant roots, and play an important role in improving plant growth and maintaining ecosystem stability. In order to discover new species and complement and improve the classification system of AM fungi, we used high-throughput sequencing to study species composition and the ecological distribution of AM fungi in the rhizosphere of Ammopiptanthus mongolicus and associated plants. Eighty-nine operational taxonomic units of AM fungi belonging to 5 classes, 3 orders, 6 families, and 9 genera including Glomus, Funneliformis, Diversispora, Claroideoglomus, Rhizophagus, Septoglomus, Scutellospora, Ambispora, and Paraglomus were identified. With regard to quantification at the genus level, high throughput sequencing was more sensitive than morphological evaluation. Ammopiptanthus mongolicus had a greater richness and diversity index than other associated plants. The ACE and Chao1 indices of AM fungi were higher in the 20-40 cm soil layer than in the 0-20 cm layer. However, the Simpson and Shannon indices were higher in the 0-20 cm layer. AM fungal abundance and diversity index were higher in Dengkou site than in Wuhai site. Redundancy analysis showed that the ACE and Chao1 indices of AM fungi were significantly positively correlated with soil-available N, but negatively correlated with acid phosphatase. Simpson and Shannon indices were significantly positively correlated with alkaline phosphatase, and significantly negatively correlated with pH. Together, these data show that the species diversity of AM fungi was higher in Ammopiptanthus mongolicus than in its associated plants. Furthermore, they reveal that interactions of host plant and soil depth had a significant effect on the community composition of AM fungi.