In the frame of a research project aiming at detection and control of Fusarium and related mycotoxins in banana fruits and maize in China, plant samples were collected in four provinces. In the southern provinces of Hainan and Yunnan, cultivated and wild banana plants coexist, together with maize. In Hubei and Henan, the Fusarium diversity was investigated on maize at the end of the growing season. Beside 14 Fusarium species, an important number of isolates belonging to the Fusarium incarnatum-equiseti complex species (FIESC) was detected. In order to understand the impact of this finding at both the genetic and mycotoxigenic levels, their phylogeny was studied on basis of the Elongation factor-1a (EF-1 a) gene, and the AFLP technique was used to provide a preliminary picture of their genetic diversity on maize.