In Morocco, saffron production plays a significant role in the local economies of certain regions and relies on high-quality planting material, strict adherence to good agricultural practices and effective post-harvest management. This study aimed to assess the quality of saffron corms used as propagation material and to identify the fungal agents associated with corm rot in the main saffron-growing areas of Taliouine and Taznakht, using an integrated approach combining morphological and molecular analysis. Surveys conducted in 2022 let to the isolation of a fungal complex from necrotic tissues of infected corms. Two species within this complex, Penicillium aeris and P. egyptiacum, were identified and confirmed as the causal agents of saffron corm rot marking their first report in Morocco. Pathogenicity tests demonstrated their ability to induce typical symptoms characterized by both superficial and internal rotting. These findings fill a major gap in the understanding of saffron diseases, provide new insights into the etiology of corms rot, and lay the foundation for developing targeted strategies to prevent and control this disease, ultimately contributing to the preservation of crop yield and commercial value.