Click-beetles (Coleoptera: Elateridae) are an abundant, diverse, and economically important beetle family that includes bioluminescent species. To date, molecular phylogenies have sampled relatively few taxa and genes, incompletely resolving subfamily level relationships. We present a novel probe set for anchored hybrid enrichment of 2260 single-copy orthologous genes in Elateroidea. Using these probes, we undertook the largest phylogenomic study of Elateroidea to date (99 Elateroidea, including 86 Elateridae, plus 5 non-elateroid outgroups). We sequenced specimens from 88 taxa to test the monophyly of families, subfamilies and tribes. Maximum likelihood and coalescent phylogenetic analyses produced well-resolved topologies. Notably, the included non-elaterid bioluminescent families (Lampyridae + Phengodidae + Rhagophthalmidae) form a clade within the otherwise monophyletic Elateridae, and Sinopyrophoridae may not warrant recognition as a family. All analyses recovered the elaterid subfamilies Elaterinae, Agrypninae, Cardiophorinae, Negastriinae, Pityobiinae, and Tetralobinae as monophyletic. Our results were conflicting on whether the hypnoidines are sister to Dendrometrinae or Cardiophorinae + Negastriinae. Moreover, we show that fossils with the eucnemid-type frons and elongate cylindrical shape may belong to Eucnemidae, Elateridae: Thylacosterninae, ancestral hard-bodied cantharoids or related extinct groups. Proposed taxonomic changes include recognition of Plastocerini as a tribe in Dendrometrinae and Hypnoidinae stat. nov. as a subfamily within Elateridae.

A phylogeny is presented for the Elateridae, inferred from parsimony and Bayesian analyses of 175 adult morphological characters. Analyses using non gap-weighted morphological data yielded results compatible with each other and some published classifications, while gap-weighted parsimony analysis did not. Bayesian posterior probabilities for the monophyly of the Elateridae and the elaterid subfamilies Athoinae (sensu Dolin 1975), Cardiophorinae (including Exoeolus Broun), Denticollinae (sensu Stibick 1979a), Elaterinae (sensu Stibick 1979a), Hypnoidinae (sensu Stibick 1976) and Lissominae (sensu Calder et al. 1993) were less than 0.05. The bioluminescent genus Pyrophorus was found to be an apical member of the mostly non-bioluminescent Agrypninae, supporting the hypothesis of at least one independent origin of bioluminescence in the Elateridae. The closest relatives to the Cardiophorinae minus Exoeolus were found in the Negastriinae. The subfamilies Cardiophorinae + Negastriinae + Tropihypnus Reitter together rendered the Hypnoidinae (or the tribe Hypnoidini of Denticollinae) paraphyletic. Lesnelater madagascariensis Fleutiaux (the type species of Lesnelater Fleutiaux) is synonymised under the type species of Pachyelater Lesne: P. madagascariensis (Lesne) so that Lesnelater is a new synonym of Pachyelater. The genus Exoeolus Broun is transferred from the Cardiophorinae to the Hemiopinae; the fossil genus Crioraphes Iablokoff-Khnzorian is transferred to the Elaterinae incertae sedis; the fossil genera Pseudocardiophorites Dolin, and Protocardiophorus Dolin are transferred to Elateroidea incertae sedis. Dolin’s (1976) hypothesis of a Jurassic origin of the Cardiophorinae was not supported by fossil evidence.

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Elateridae represents one of the largest families within Coleoptera, yet their interrelationships remain under‐investigated. Molecular data are missing for most lineages, especially for the species‐poor suprageneric taxa. In this study, we investigated the limits and phylogenetic position of Pityobiinae sensu Calder (1996), a group of several small genera from the New World and Australasia, using maximum likelihood and Bayesian inference methods. We merged new sequence data with those deposited in GenBank, producing a final matrix of 178 terminal taxa and covering the main click‐beetle subfamilies. The resulting topologies showed Elaterinae as sister to remaining click‐beetle lineages, and Agrypninae as sister to the Morostomatinae + Dendrometrinae + Cardiophorinae + Negastriinae clade. Members of Hemiopinae, Lissominae, Thylacosterninae and Pityobiinae formed basal lineages within Elateridae − Elaterinae. We found Lissominae to be polyphyletic, including Thylacosterninae as a terminal lineage and with Oestodini forming an independent lineage outside that clade. Therefore, the subfamily Oestodinae stat. nov. was reinstated for the North American genera Oestodes LeConte and Bladus LeConte. The Australian genera Dicteniophorus Candèze, Drymelater Calder and Stichotomus Candèze were transferred from Dendrometrinae to Elaterinae. Pityobiinae was recovered as two distant lineages in all analyses and correspondingly the subfamily is reduced to contain only the North American Pityobius LeConte and tentatively the South American Tibionema Solier, for which we have no DNA sequences. Additionally, we propose Parablacinae subfam. nov. for the remaining former pityobiine genera from Australia and New Zealand. The new subfamily includes Parablax Schwarz, Metablax Candèze, Wynarka Calder, Xuthelater Calder, Tasmanelater Calder, Parasaphes Candèze and also Ophidius Candèze, which is transferred here from Elaterinae. We failed to find universally diagnostic synapomorphies in adult morphology for Parablacinae, a common problem in elaterid taxonomy. Future research, including a comprehensive phylogeny of the subfamily and re‐examination of the morphology of its species is crucial to understanding the limits and classification of this lineage.

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