Fusarium spp. is one of the most prominent genera of plant pathogens due to its wide range of hosts and mycotoxin production. The Fusarium fujikuroi species complex (FFSC) encompasses several known plant pathogens, such as Fusarium circinatum, F. fujikuroi, F. sacchari, and F. verticillioides. Cymbopogon citratus is a widely distributed aromatic and medicinal plant rich in secondary metabolites. Most of C. citratus cultivation is related to essential oil (EO) extraction since their volatiles have applications in the food, fragrance, and pharmaceutical industries. In the present study, the first report of C. citratus wilt caused by a FFSC species in Portugal is described. Symptomatologic, cultural, morphologic, genetic, and cytogenomic characteristics associated with this pathogen and disease are displayed. The cultural features included flat, white-colored colonies with filiform margins and abundant cottony aerial mycelia at the upper surface and orange-violet colored at the lower surface. On Carnation Leaf-Piece Agar, septate fusoid macroconidia were present, displaying a flattened tapering toward the basal part and a number of septa ranging from one to four. The comparison of amplified and aligned ITS sequences revealed a 100% similarity between the isolated fungus and the FFSC. Finally, a flow cytometry assay revealed an estimated genome size of 29.9 Mbp, contrasting with other FFSC-known pathogens. Ultimately, by examining these various aspects, this work aims to comprehensively understand the wilt and its causal agent.