Mycorrhizal fungi play a key role in supporting plant communities in nutrient-poor environments, yet their diversity and distribution in Amazonian floodplain forests remain poorly understood. In this study, we assessed mycorrhizal fungal communities across three blackwater igapó forests in Central Amazonia—RDS Uatumã, RDS Rio Negro, and PARNA Jaú—using DNA metabarcoding of root samples. We examined how flood regimes and local environmental conditions influence the richness and composition of arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (ECM). We found 568 mycorrhizal ASVs, including 307 ECM and 238 AMF. Mycorrhizal richness was higher in low igapós, which experience prolonged inundation. However, ECM richness showed site-specific patterns. Community composition varied across sites and flood levels, with distinct fungal assemblages associated with different host trees. Our results suggest that a complex interplay of flood dynamics, local characteristics, and plant-fungal interactions shapes the structure of mycorrhizal communities in igapós. Despite the harsh conditions of seasonal flooding, these forests harbor a diverse and specialized mycorrhizal biota, including a high number of ECM lineages rarely documented in tropical wetlands. This study contributes with novel insights into Amazonian belowground biodiversity and highlights the importance of topographic and hydrological heterogeneity in maintaining adapted fungal diversity and function. Understanding these patterns is critical for forecasting the ecological impacts of climate-driven changes to Amazonian flood regimes.