The genus Fusarium consists of multiple diverse species, which, as a result of their frequency in nature and pathogenicity, are significant in agriculture, as well as in human and veterinary medicine. In the course of field trials, by using standard phytopathological methods, and performing analyses of 19 different varieties of wheat and a portion of infected grains gathered from two distinct locations in Slovenia, we have determined the presence of various phytopathogenic species of the genus Fusarium. Because of the reliability, the experiment was performed in two consecutive years, 2012 and 2013. A laboratory analysis was conducted with an ELISA test on all grain samples for the determination of deoxynivalenol (DON) concentration. The results show that the main differences in the infection levels (F. culmorum + F. graminearum; FC + FG) of wheat samples were found in Jable (humid area), at the same time showing higher levels of DON content than Rakičan (dry area). Such a statement is supported by correlation test, where correlation is evident between FC + FG and DON in every variation. The data for both wheat types (awned and awnless) together showed that the grain in Jable is statistically significant more infected by FC + FG when compared to that in Rakičan. Moreover, our descriptive analysis confirms that the infection rate of grain with FC and FG shows a strong correlation with the emergence of DON.