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Tomato fusarium wilt, caused by Fusarium oxysporumf. sp. lycopersici, is a widespread disease occurring in majority of tomato cultivation areas worldwide. Homeobox transcription factor-encoding genes play a vital role in fungal vegetative growth and morphology, but their role in fungal pathogenicity is largely unknown. In this study, 25 homeobox genes (FoHOX 1–25) were identified in the F. oxysporumf. sp. lycopersicigenome, using bioinformatics methods. Phylogenetic analysis showed that the FoHOXgenes were divided into four groups; furthermore, these genes were unevenly distributed on six chromosomes and qRT-PCR analysis revealed that all 25 were differentially expressed in the host during plant-pathogen interaction. During our study, expression levels of the respective genes in tomato seedlings increased from day one to seven, and most genes showed a decreasing expression trend by day ten. In conclusion, these results may provide a useful foundation for functional analyses of homeobox transcription factor genes involved in the pathogenicity, and regulation of plant immunity.