Fusarium spp. are among the most common fungal species associated with diseases both on wild and cultivated plants, including sunflowers. They infect all plant tissues causing damage to roots, bundle vessels, stems, leaves, and seeds, often causing significant yield losses. Because contaminated seeds can spread diseases into new areas and transmit them to growing plants, the quality and sanitary status of the seeds are the key to limit the spread of the disease. This study aimed to identify and determine the prevalence of Fusarium species associated with sunflower seeds and access their transmission to growing plants. A set of 49 Fusarium isolates was collected from seeds of eight sunflower cultivars. They were characterized through morphological, cultural, and genetic features. Genetic diversity was estimated through amplification of the elongation factor gene (EF-1 α), which also served to select representative isolates to perform amplification of the β-tubulin 2 gene (TUB2). There were identified four species of Fusarium (i.e., F. fabacearum, F. proliferatum, F. pseudocircinatum and F. verticillioides) that caused seed rot, vascular darkening, withering, malformation, and stunting of growing sunflower plants. Among them, F. proliferatum was the most prevalent species. Our results highlight that various species of Fusarium are associated with damage on sunflower seeds and all of them can be transmitted through infected seeds and cause disease in growing plants.