Endomycorrhizas or arbuscular mycorrhizal fungi (AMF) are microfungal associates known to facilitate nutrient absorption in higher plants that benefit growth and survival. Studies have shown that they can induce systemic host resistance against pathogenic fungi, but little information is known about its contributions to gall rust disease in Falcataria moluccana, an important plantation tree species. This paper investigated the community of endomycorrhizas under F. moluccana stand affected by Uromycladium rust from a secondary-growth forest in Laguna, Philippines. Three transects (1.5 km) were established wherein matured F. moluccana trees (n = 32) were assessed for gall rust incidence and disease severity index (DSI) using a five-point rating scale to categorize infection. Composite rhizosphere samples were collected from nine sampling plots for macronutrient analysis and AMF assessment. Endomycorrhizal spores were isolated from dissolved 100-g soil solution following wet-sieving and decanting method then characterized morphologically for identification, spore density, and diversity analysis. Results of the tree health survey showed 100% disease incidence with moderate infection (DSI = 30–44). Overall, 13 morphospecies of endomycorrhizal fungi were identified from three orders and five families. The eight genera associated with F. moluccana were Acaulospora, Ambispora, Diversispora, Enthrophospora, Funneliformis, Gigaspora, Glomus, and Rhizophagus. The Shannon diversity index (H’) revealed a significant (p< 0.002) difference in all sites [F (2, 31) = 7.46]. The findings suggest that species abundance and density of AMF fungi are related to soil phosphorous and the severity of gall rust. This study presents the potential of important AMF species for the integrated management of gall rust disease affecting F. moluccana.