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ABSTRACT Marginal soils affected by salinity, sodicity and alkalinity decrease crop productivity. In this context, a viable alternative strategy lies in the remediation of degraded lands using beneficial microorganisms. This study aims to characterize native arbuscular mycorrhizal fungal (AMF) communities by sequencing PCR amplicons that cover most of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region, and a portion of the large subunit (LSU) rRNA, employing Oxford Nanopore Technologies (ONT). Three field sites, with varying crop conditions, were selected: a patch with no crop growth (Site 1), a patch with corn stubble (Site 2), and a patch with wheat plants exhibiting 15 days of growth (Site 3). Soil analyses revealed distinct characteristics - alkaline saline sodic soil (ASS) for Site 1, moderately alkaline soil (A) for Site 2, and neutral soil (N) for Site 3. ONT sequencing yielded a total of 4,040,470 raw reads from which 19.13% survived after quality and length filter. Reads were grouped in 556 clusters, of which 222 remained after bioinformatic analysis. Despite moderate error rates in 9.4.1, flowcells chemistry, using a clustering and polishing approach facilitated the ecological analysis and allowed a better taxonomic resolution. Bioinformatic analysis showed no significant differences in AMF diversity among soils. However, results suggest the dominance of Glomeraceae and Acaulosporaceae families, specifically the genera Glomus and Acaulospora in ASS soil. Further exploration is required to better understand their role in promoting plant growth under adverse conditions. The study highlights the significance of cutting-edge sequencing tools in advancing the comprehension of essential symbiotic relationships for sustainable agriculture in challenging environments.