The north‐east of Brazil is one of the most important melon‐producing regions in the world. Crop yield is often reduced by the occurrence of a root rot disease, caused by Fusarium species. The present study aimed to characterize a collection of 31 isolates with morphological markers of F. solani obtained from melon plants with symptoms of root rot by phylogenetic analysis of the barcode regions EF‐1α and RPB2, and to verify their pathogenicity to melon plantlets. Phylogenetic analysis showed that 29 isolates grouped with reference material of Fusarium falciforme (FSSC 3 + 4) and two with F. suttonianum (FSSC 20). The pathogenicity test showed that isolates of both species cause root rot in melon plants, with no significant difference of virulence between isolates and species with both methodologies used (infested toothpick and infested rice). Melon plants expressed first symptoms 15 days after inoculation, showing yellowing and wilting, with later tipping and rot. To our knowledge, this is the first report of the occurrence of these species causing root rot in muskmelon in Brazil. Our results support monitoring of causal agents of melon fusarioses and will be useful for breeding programmes in the search for plant material with resistance to Fusarium rot.