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SummaryUnderstanding pathogen-agrosystem interaction is particularly essential when applying a control method to minimize pathogen prevalence prior to plant infection. To meet this requirement, frequency of major root rot pathogens isolated from bean root and seed, and their soil populations were examined in farmers’ fields. Multivariate analyses evidenced more frequent isolations of Fusarium solani and Rhizoctonia solani from root and seed compared to Macrophomina phaseolina and Fusarium oxysporum. Two Fusarium species had denser soil populations than R. solani and M. phaseolina. More frequent isolations of pathogens were detected in root and seed collected from Abhar and Khodabandeh compared to Kheirabad region. Agronomic and soil variables corresponded less closely to root infections compared to soil infestation and seed infections. Bean market class, herbicide application, and planting depth were linked to root, seed and soil infestations. Such information provides a basis for increased confidence in choosing appropriate control strategies for a pathogen and region in sustainable agriculture.