Elmidae (Coleoptera: Byrrhoidea) comprises diverse groups of specialized aquatic beetles, but the phylogenetic positions of the intrafamilial taxonomic groups remain unclear. We performed phylogenetic analyses of 26 genera and 73 elmid species and subspecies representing four of the five currently recognized tribes from Holarctic region (Japan, Europe and North America) using sequence data from up to 585 ultraconserved elements (UCEs). The UCE-based phylogenetic trees inferred by both maximum-likelihood and Bayesian inference methods resolved most of the phylogenetic relationships with high support. Our results indicate that a revised classification for the intrafamilial taxonomic groups in Elmidae is necessary. We also examined the correspondence of the character states of ten adult and larval morphological traits to the phylogeny and identified several traits that are potentially useful for defining intrafamilial taxonomic groups in Elmidae. Based on the molecular phylogeny and morphology of adults and larvae, Gonielmis Sanderson syn. n. and Optioservus Sanderson syn. n. are synonymized with Heterlimnius Hinton. Nomuraelmis Satô syn. n. was also synonymized with Stenelmis Dufour. A revised checklist and an identification key to the species groups are provided for Heterlimnius.