Water mites of the Hygrobates fluviatilis-complex are common and often the most abundant water mite group in running waters in the Palaearctic. This study provides the first time-calibrated phylogeny of this complex to date. Fossil-calibrated modelling reveals that the most recent common ancestor of the H. fluviatilis-complex originated in the Oligocene. Phylogenetic and dating analyses show the presence of three monophyletic lineages within the H. fluviatilis-complex, with the H. turcicus-clade as the earliest branching lineage. The diversification and speciation processes mainly started from the Oligocene-Miocene around 24 million years ago and continued during the Miocene. In this study, we tried to link time frames of boundary diversification and appearance of certain species with particular paleogeological events. We found evidence of multiple colonization of Corsica in different phases of its geological history, resulting in the presence of two endemic lineages, H. corsicus and H. cyrnusensis sp. nov., the latter species is described by an integrative approach in this study.