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Fusarium oxysporum is a famous plant pathogenic filamentous fungus. Here, we report the complete mitochondrial genome sequence of F. oxysporum f. sp. lactucae isolated from the lettuce field in Suwon area, Korea. Total length of the mitochondrial genome is 45,020 bp and it encodes 42 genes (15 protein-coding genes, two rRNAs, and 25 tRNAs). Nucleotide sequence of coding region takes over 32.7%, and overall GC content is 32.4%. Phylogenetic tree presented that F. oxysporum f. sp. lactucae 09-002 was clustered with Fusarium commune not like another F. oxysporum mitochondrial genomes, requiring further analyses.