Abstract Malachiinae (Coleoptera: Malachiidae), commonly known as true soft‐winged flower beetles, are widely distributed across the globe except New Zealand. It is the largest subfamily of Cleroidea (over 3000 species) and is currently divided into seven tribes, among which the relationships are hard to assess due to their bizarre morphological modifications in males. Although a few molecular phylogenetics were attempted, they were all constructed on basis of four or five short nucleotide fragments, which may not contain enough phylogenetic information, thereby resulting in unclear relationships. To investigate the phylogenetic relationships among the tribes within Malachiinae, low‐coverage whole genomes of 26 species from the superfamily Cleroidea were sequenced and analysed, including 22 species of Malachiinae. The mitochondrial genomes (mitogenomes), nuclear genes ( 18S , 28S rRNA) and universal single‐copy orthologs (USCOs) were obtained as molecular markers from low‐coverage sequencing data. A total of 24 complete or nearly complete mitochondrial genomes of Malachiidae species were annotated and analysed. Further combined the newly sequenced data and those available in the public database, four different data matrices were analysed by different methods to reconstruct the phylogeny of Malachiinae. The results indicated that these phylogenetic analyses produced consistent topologies, and the phylogenetic relationships within Malachiinae were recovered as (Illopini + (Troglopini + (Colotini + Apalochrini))) + (Ebaeini + (Attalini + Malachiini)).

A preliminary phylogeny of Malachiinae (Coleoptera, Malachiidae): From multiple genes to whole genomics