Beauvericin (BEA) and enniatins (ENNs) are a group of hexadepsipeptides mycotoxins produced by several species of Fusarium, which show strong toxic effects on epithelial cells, immune cells and ovarian cells. The morphology and the molecular genetic characteristics of toxin-producing Fusarium species are introduced, as well as the environmental conditions, such as temperature and substrate, which can influence BEA and ENNs production. The differences in genetic level and the amino acid level about synthetase of two types of mycotoxins, and their influencing factors about mycotoxin-producing Fusarium species are expounded emphatically. It will provide a theoretical basis for the prevention and control of two types of mycotoxin and mycotoxin-producing Fusarium species.