Banana (Musa spp.) is one of the most significant horticultural crops due to its economic and social value to communities across the globe. A major constraint to the worldwide cultivation of banana is the disease Fusarium wilt or Panama disease, which is caused by the soilborne fungal pathogen, Fusarium oxysporum f.sp. cubense (Foc). Currently, the molecular mechanisms underpinning the pathogenicity of Foc remain largely unknown. In this study, we sought to investigate the genetic mechanisms regulating pathogenicity in Foc. In initial studies, we identified the distribution and sequence diversity of a class of fungal effector genes termed the secreted in xylem (SIX) genes in a collection of isolates representing the various genetic lineages of Foc. This work demonstrated that the repertoire of SIX genes within a Foc lineage is highly conserved however isolates of Foc from genetically distinct lineages carried unique ranges of SIX genes. A systematic analysis of the SIX gene homologues identified in Foc also supports the hypothesis that this class of fungal effectors has been horizontally acquired in the lineages of Foc. Currently, it is hypothesised that small, secreted proteins, such as the SIX proteins, confer the host- and cultivar-specific pathogenicity of the lineages of Foc. We further investigated this hypothesis by attempting to alter the cultivar-specific pathogenicity of Foc by modifying the complement of SIX genes through genetic transformation. Ongoing studies are being performed to investigate the genomic organisation and evolution of Foc and the localisation of the SIX genes in the genome of Foc using long-read sequencing technology. This work has particular significance for understanding how Fusarium oxysporum has evolved and adapted to a crop system as well as investigating the molecular interaction between pathogens and their hosts.