Trichothecene genotype composition, mycotoxin production, genetic diversity, and population structure were analyzed, using 185 Fusarium strains collected from wheat (Triticum aestivum L.) throughout the Jiangsu province during 1976, 1983, 1998, 2006, and 2014. The results showed that 3-acetyldeoxynivalenol (3ADON) was consistently the predominant type in this region over 40 years, and the nivalenol (NIV) type has emerged since 1998. Long-term rotation of wheat and rice (Oryza sativa L.), rather than fungicide application, crop fitness, or weather conditions, might be the main cause of this phenomenon. The genetic diversity results from two toxin synthetic genes, Pks4 and Tri10, and variable number of tandem repeat (VNTR) markers revealed the largest variance within the population in 1998, which was also the year with the highest production of mycotoxins. Population differentiation analysis indicated that major temporal population comparisons from the same area were not significantly differentiated. Our results showed that dominant species could maintain genetic stability for a long time, and Pks4 would be of utility in genetic and population studies.Fusarium head blight (FHB) is one of the most destructive and widespread diseases of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), and other cereals, globally. This disease reduces crop yields, causing extensive economic losses. More importantly, harvested grain quality is often compromised, due to mycotoxins produced by pathogens. Consumption of contaminated grains and products might have pernicious effects on human and animal health 1 . Fusarium graminearum species complex (FGSC) consists of at least 16 phylogenetically distinct species, and is the main causal agent of FHB [2][3][4][5][6][7] . Fusarium asiaticum is the predominant species in Asia 8-12 , while F. graminearum sensu stricto (s. str.) is present in most FHB-occurring areas around the world, especially in America and Europe 3,4,6 . Members of FGSC produce toxic secondary metabolites, among which trichothecene and zearalenone (ZEN) are the most closely monitored due to their high detection rates and strong toxicity. Trichothecene toxins, including deoxynivalenol (DON) and nivalenol (NIV), inhibit eukaryotic protein biosynthesis and cause some human and animal mycotoxicoses 13,14 . FGSC strains have been shown to possess one of three trichothecene genotypes: 3-acetyldeoxynivalenol (3ADON), or NIV 15 . Zearalenone (ZEN) and its metabolites have estrogen-like functions and strong teratogenic effects 16 . Moreover, ZEN has been shown to be genotoxic to cells and toxic to some animal tissues 17 . As a result, the mycotoxin-producing ability of individual isolates is always a concern.With the development of molecular biology, sequences and functions of members in the trichothecene biosynthetic gene cluster have been gradually elucidated. The first gene discovered in the trichothecene pathway was Tri5 18 , which catalyzes the first reaction in this pathway. Thereafter, the other 11 core genes...