Fusarium strains isolated from the different plant hosts and formerly identified as Fusarium subglutinans s. l. according to morphological characteristics were analyzed in detail. Based on phylogenetic analysis of three loci (TEF, tub, and RPB2) two strains isolated from stem of wheat and root of rape were re-identified as F. temperatum. This is first report of rape and wheat as a novel plant host for F. temperatum that mainly associated with maize. This is also the first detection of F. temperatum in Russia. Other strains turned out to be F. subglutinans s.str. The examination of morphological characters has not revealed remarkable variation between the species: the features of F. temperatum and F. subglutinans are sufficiently similar to exclude confidence in identification based on visual assessment. Two F. temperatum strains possess alternate MAT idiomorphs, whereas the both F. subglutinans strains contain only MAT-1 idiomorph. Fertile crossings were observed between two F. temperatum strains in the laboratory conditions. Both F. temperatum strains produced beauvericin in high amounts of 1665 and 6106 μg kg-1 in contrast to F. subglutinans strains. Additionally, one F. temperatum strain produced 3407 μg kg-1 moniliformin. No one from the analyzed strains produced the fumonisins. The differentiation of the F. temperatum and F. subglutinans species is possible only with the involvement of molecular genetics and chemotaxonomic methods.