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Aim: Alexander von Humboldt observed that plant communities on different continents but under similar climatic conditions shared few common species but often contained representatives of the same genera or higher taxonomic groups. To test if this observation can be extended to substrate type, we explored whether a phylogenetic signature could be seen among floras growing on ultramafic substrates that present challenging edaphic conditions for plant growth and are well‐known for their distinctive vegetation. Location: Cuba, Madagascar, New Caledonia. Taxon: Angiosperms. Methods: We compared the floras of Cuba, Madagascar and New Caledonia to test whether the same plant families were under‐ or over‐represented on the ultramafic substrates of the three islands. Results: Pairwise comparisons showed that plant orders and families tended to have the same behaviour on the three islands, i.e. ultramafic substrates filtered (in favour of or against) the same plant groups in the three biogeographical distinct areas. The COM clade (comprising Celastrales, Oxalidales and Malpighiales) appears to be over‐represented on ultramafic substrates in all three islands and contains over half of the world's known nickel hyperaccumulators. Main conclusions: Our analyses provide support for Humboldt's observation by showing that ecological sorting can favour the same plant lineages in similar environments in different biogeographical regions. [ABSTRACT FROM AUTHOR]