Background: Allergic fungal sinusitis (AFS) and eosinophilic mucin rhinosinusitis (FARS) represent pathophysiological variants of sinusitis and have similar clinical features. However, to date, few studies have described the differential diagnosis of AFS and EMRS in detail. We therefore investigated the use of magnetic resonance imaging (MRI) in the differential diagnosis of AFS and EARS. Methods: Ninety-three patients (aged 13-75 years) with sinusitis and AFS or EMRS established according to pathological, clinical, or laboratory examinations were enrolled. Each patient was evaluated for demographic and clinical characteristics, fungal-specific immunoglobulin E, peripheral blood eosinophils, histopathology of the sinuses, as well as signal attenuation within the opacified sinuses on computed tomography and MRI scans. Results: Thirty patients presented with AFS and 63 with FARS. The histopathological characteristics of the secretion and mucosa in the affected sinuses, but not the absolute counts or percentage of blood eosinophils, differed between the 2 groups. The presence of asthma was significantly higher in the EMRS group, whereas allergy to fungi and T2-weighted MRI signal attenuation were significantly increased in the AFS group. Conclusions: MRI features are key to the differential diagnosis of AFS and EMRS.