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Fragaria L. and Rubus L. are two Rosaceae genera with strikingly different levels of taxonomic diversity (20 vs. ~500 species, respectively), yet with similar processes likely at play in their evolution—polyploidisation, hybridisation and apomixis. Each genus contains important soft fruit crops—garden strawberry in Fragaria, red raspberry and blackberries in Rubus. Furthermore, congeneric wild species have been used as a source of agronomically beneficial alleles. Both Rubus and Fragaria display well-supported monophyly, but resolution below the subgenus level in Rubus and beyond the two main clades in Fragaria is limited. More comprehensive sampling of plant genomes at a population level combined with more sophisticated models of phylogenetic inference is required for complete detangling of the reticulate genealogies in Fragaria and Rubus.