Elateriformia consists of Dascilloidea, Buprestoidea (jewel beetles), Byrrhoidea and Elateroidea (click beetles, fireflies and relatives). Numerous elateroid lineages contain taxa with modified metamorphosis resulting in sexual maturity while retaining larval characters. Additionally, they evolved unique defensive strategies including clicking mechanism, aposematic coloration and bioluminescence. To investigate the phylogenetic position of Elateroidea within Coleoptera, we merged 1048 newly produced 18S rRNA, 28S rRNA, rrnL mtDNA, and cox1 mtDNA sequences for ∼300 elateriform taxa with data from GenBank. The 975-taxa dataset aligned in BlastAlign was analyzed under maximum likelihood criterion. The results agreed in most aspects with the current morphology-based classification and results of molecular studies. Elateriformia were monophyletic and Elateroidea were sister to Byrrhoidea. Further, we analyzed all-data (513 elateriform taxa) and pruned matrix (417 elateriform taxa, all fragments present) using parsimony and maximum likelihood methods to reveal the phylogenetic relationships among elateroid lineages and examine the evolution of soft-bodiedness, neoteny and bioluminescence. We confirmed the monophyly of Elateroidea sensu lato and most of the families, with Telegeusidae inferred in most trees within paraphyletic Omethidae. The clade Artematopodidae+Telegeusidae+Omethidae was a sister to remaining elateroids. All topologies reject the relationships of hard-bodied Elateridae, Eucnemidae, Throscidae and Cerophytidae, formerly supposed to be a monophylum. Eucnemidae and Throscidae formed independent lineages and the position of Cerophytidae was variable - either a sister to Throscidae, or an independent lineage. The Lampyridae+Cantharidae clade was in most trees sister to Phengodidae+Rhagophthalmidae+Omalisidae+Elateridae. Molecular phylogeny of Elateroidea confirmed the multiple origins of soft-bodied, neotenic and light emiting lineages. On the basis of our molecular phylogeny, we place former Telegeusidae as a subfamily in Omethidae.