Healthy plant tissues provide a dynamic habitat for endophytes, which are a promising source of secondary metabolites and bioactive natural products. This study explores the fungal diversity of saffron corms to assess its potential impact on plant growth and health. Saffron corms were analyzed in the laboratory, leading to the identification of Monocillium ligusticum, a slow-growing isolate (28–33 mm in diameter after one month). Due to the morphological similarity between isolates, molecular techniques were used for precise identification, confirming the presence of Monocillium in saffron tissues. The Monocillium ligusticum isolate was registered in a national database and deposited in GenBank (OM980234). Pathogenicity tests showed that this strain is non-pathogenic to saffron corms, suggesting it poses no threat to the plant. These results provide new insights into positive fungal/plant interactions and open promising prospects for using endophytic fungi to improve plant production and protection.