idiomorph, from the same or different Fusarium species, coincided in the same field of several sites. Selected sequences of both idiomorphs showed greater divergence between species than within the same species. These changes were greater in the noncoding regions than in the coding regions. The variation of the mating type genes and the coexistence of both idiomorphs in the same agricultural site, point to a potential future change in the virulence of Fusarium isolates. In general, these findings will help to better understand the genetic variability of some Fusarium species in Mexico.