Taxonomic changes are made based on checkered beetle (Coleoptera: Cleridae) types of the Natural History Museum, London (BMNH).Lectotypes are designated (and holotypes and paralectotypes recognized) for 44 species of Hydnocerinae, including the type species for Isolemidia, Parmius, Paupris, Allelidea, Blaesiopthalmus and Lemidia, four species of Enoclerus (Clerinae), and 14 species of Cymatodera (Tillinae). Annotations include comments on additional type material, new type locality, previous (type series) locality, and questionable or missing types. Phyllobaenus pallipes(Gorham) and P. rufithorax (Gorham) are synonymized with P. flavifemoratus(Gorham), P. chapini (Wolcott) is synonymized under P. lateralis (Gorham), and P. villosus (Schenkling) is synonymized under P. longus (LeConte), new synonymies. The first molecular phylogeny of the clerid lineage (Coleoptera: Cleridae, Thanerocleridae) is presented and compared with the two most recent phylogenetic hypotheses of the group. Phylogenetic relationships of checkered beetles wareere inferred from approximately 5,000 nucleotides amplified from four loci (28S, 16S, 12S, COI). A worldwide sample of ~70 genera is included and phylogenies are reconstructed using Bayesian Inference and Maximum Likelihood. The results are not entirely congruent with either of the current classification systems. Three major lineages are recognized. Tillinae are supported as the sister group to all other subfamilies, whereas Thaneroclerinae, Korynetinae sensu latu and a new subfamily formally described here, Epiclininae, new subfamily, form a sister group to Clerinae + Hydnocerinae. To assess the phylogeny and evolution of Hemiptera, a comprehensive mitogenomic analysis integrating mitogenome-based molecular phylogenetics, fossil-calibrated divergence dating (using BEAST), and ancestral state reconstructions are presented. The 81 sampled mitogenomes represent the most extensive mitogenomic analyses of Hemiptera to date. The putatively primitive “Homoptera” was previously rendered paraphyletic by Heteroptera, whereas the presented results support each group as monophyletic. The results from both diet and habitat ancestral state reconstructions support that 1) Heteroptera (and Homoptera) evolved from a phytophagous ancestor, contrary to the popular hypothesis that the ancestor was predaceous; and 2) family-level radiation of Heteroptera is coincident with the apically-produced labium and the novel hemelytron. It is here proposed these morphological innovations facilitated multiple independent shifts from phytophagy to predation and multiple independent colonizations of aquatic habitats.