Fusarium oxysporum ff. sp. canariensis (Foc) and palmarum (Fop) cause lethal fusarium wilt on ornamental palms. Foc infects Phoenix canariensis and has a worldwide presence, whereas Fop primarily infects Washingtonia robusta and Syagrus romanzoffiana and is currently primarily restricted to Florida (USA). A Secreted in Xylem (SIX) gene profile was obtained for Fop and Foc isolates from the USA. SIX1, SIX7, SIX10 and SIX12 were detected in most Foc isolates and, with the exception of SIX12, with minimal sequence polymorphism. SIX8 and SIX9 were detected in all Fop isolates, with no sequence polymorphism. SIX10 was also present in seven of the Fop isolates. Phylogenetic trees were constructed using EF-1α‐, SIX1, SIX7 and SIX10 gene sequences from this study and previously derived sequences from Foc isolates obtained in Australia, the Canary Islands and Japan. The topology of the housekeeping EF‐1α gene indicated Foc is polyphyletic, with the Australian isolates separating into a distinct group from all other Foc isolates. However, the topologies of SIX1, SIX7 and SIX10 phylogenetic trees for Foc indicate monophyly. As has been proposed previously, this suggests the core genome of Foc evolved into a separate lineage after the SIX genes were conserved within the whole genome. This study is the first to generate SIX12 sequences for Foc. Interestingly, the topology of the SIX12 phylogenetic tree suggests polyphyly. For Fop, the topologies of the EF‐1α, SIX8 and SIX9 phylogenetic trees support monophyly. The distinct SIX gene profile and EF‐1α sequence of Fop demonstrates an independent evolutionary origin from Foc.