Fusarium temperatum Scaufl. & Munaut is one of the most important fungal pathogens that cause ear and stalk rots in maize. In this study, we sequenced genomes of two F. temperatum isolates (KFI615 and KFI660) isolated from corn ears in Poland. A total of 110.3 and 116.3 million 100-nucleotide paired-end clean reads were obtained for KFI615 and KFI660, which were assembled into 20 and 18 scaffolds with an estimated genome size of 45.21 Mb and 45.00 Mb, respectively. These genome sequences provide important resources for understanding pathogenicity and biology of the pathogens within the Fusarium fujikuroi complex.