The carnation is one of the most important products for export in the floriculture industry of Colombia. Fusariosis (a disease resulting from presence of Fusarium) appears on the crops in two forms: vascular wilt and basal rot. The first is caused by Fusarium oxysporum f. sp. dianthi, which is a well-characterized disease. The second, caused by Fusarium verticillioides (previously Fusarium roseum), is a non-characterized disease and its development in the plant has not been described in detail. The symptoms of basal rot were differentiated from vascular wilt, through infection of plants in the greenhouse, with isolates of F. verticillioides and F. oxysporum obtained from lesions of symptomatic plants. The fungi morphological characterization allowed differentiation of the isolates of these two species and their growth habits on different media. The sequencing of 8 different genes with more than 13 amplicons in the 2 species showed genetic differences that grouped the isolates into different taxa. Multilocus sequence typing analysis using DNA sequences of 8 different genetic regions confirmed the presence of F. verticillioides. In this study, the role of F. verticillioides was demonstrated in the stems of carnation in commercial crops that presented pathogenic lesions. According to the results of the study, F. verticillioides is the etiological agent that produces the basal rotting in carnation plants, alone or in association with F. oxysporum.