Acha (Digitaria spp.) is a nutritionally valuable cereal widely cultivated in West Africa. However, fungal contamination frequently compromises its production and postharvest quality. This study investigated the fungal species associated with diseased acha seeds marketed in Sokoto State, Nigeria, using a combination of morphological and molecular approaches and assessed their pathogenicity on healthy seeds. Diseased seed samples were collected from three major markets; Wamakko, Bodinga, and Gwadabawa and subjected to fungal isolation on potato dextrose agar. Pure isolates were morphologically identified, followed by molecular characterization via PCR amplification of the ITS region, sequencing, and BLAST analysis. Pathogenicity tests were conducted by inoculating healthy seeds with isolated fungi spore suspensions under controlled conditions. A total of 150 seeds were sampled. 80 of 150 were infected, with Aspergillus niger, Fusarium oxysporum, and Penicillium spp. identified as the predominant species. PCR amplification successfully confirmed the presence of ITS sequences, and BLAST analysis validated species identity, including P. citrinum. Pathogenicity assessments revealed that all isolates induced disease symptoms, with A. niger exhibiting the highest severity, followed by F. oxysporum and P. citrinum. Fungal diversity varied across locations, with Gwadabawa exhibiting the highest species richness. These findings highlight the prevalence and pathogenic potential of fungal contaminants in marketed acha seeds and underscore the importance of integrating molecular diagnostics and improved storage practices to reduce postharvest losses, ensure seed quality, and safeguard public health.