An extensive combined data set comprising 160 morphological characters of adults and immature stages of Hydrophiloidea and sequences of six different genes were analysed using parsimony and a Bayesian approach. Analyses were carried out with equal weight for individual morphological and molecular characters, and alternatively with approximately equivalent weight for the entire partitions, i.e., 147 informative morphological characters × 9.5 ≈ 1383 informative molecular characters. With the former approach some conventional groups such as the histeroid lineage (Histeridae and Sphaeritidae), Helophorinae and Sphaeridiinae were recovered. However, the branching pattern as a whole is strongly in contrast to the results of previous studies. The results obtained with the modified weighting scheme (9.5:1) conform more to morphology based analyses. The monophyly of Hydrophiloidea, Histeridae + Sphaeritidae, Epimetopinae + Georissinae, Helophorinae, Sphaeridiinae and of the hydrophiline-sphaeridiine lineage is supported in the parsimony analysis. Spercheinae is placed as sister group of all the remaining hydrophiloid groups and a clade is formed by the subfamilies Epimetopinae, Georissinae, Hydrochinae and Helophorinae. In the Bayesian analysis the monophyly of Hydrophilidae is supported. Georissinae form a clade with Hydrochinae, and Epimetopinae are placed as sister group of a clade comprising Spercheinae + the hydrophiline-sphaeridiine lineage. Berosus is placed as the sister group of the remaining groups of Hydrophilinae-Sphaeridiinae in both analyses, and Sphaeridiinae are always nested within a paraphyletic Hydrophilinae. The divergent results of the different analyses show that important questions in the phylogeny of Hydrophiloidea such as for instance the placement of Spercheinae are still open.