J Appl Genetics (2012) 53:227–236 GenBank (results not shown), than to those present in the isolates from the Polish population of F. equiseti (Fig. 5). All our results provide quite a novel insight into the intra- specific polymorphisms of the mycotoxin biosynthetic gene sequences in F. equiseti. It shows the divergence of those genes between the species but considerably higher conser- vation level inside the species. A general conclusion can be drawn that the coding sequences of mycotoxin biosynthetic genes (like TRI5) are as good target sequences for species and population discrimination as highly variable intron regions of genes widely used in phylogenetic studies (e.g. tef-1α) and, in some cases, they even have some advantages over the less diverse ones, like the ITS regions. 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