Abstract
Aim Freshwater rock pools are ephemeral and fragile habitats that support specialised animal taxa. While distributed worldwide, these habitats are usually neglected and overlooked. We used DNA metabarcoding and metaphylogeographic approaches to study inter and intraspecific tardigrade biodiversity to identify their biogeographic patterns to inform conservation measures. Location Europe. Period Present. Major Taxa Studied Tardigrades. Methods We conducted DNA metabarcoding targeting a fragment of the cytochrome oxidase subunit 1 gene of 163 freshwater rock pools from four sites in Sweden, Poland and Italy to analyse the effect of both short and long distance on their alpha diversity and genetic differentiation. Results A total of 85 tardigrades OTUs (species‐level clusters) were detected, with the most prevalent taxa across all samples being species from the genus Ramazzottius . OTUs richness was mostly driven by a negative relationship with rock pool depth and site‐specific differences. For seven OTUs a phylogeographic analyses revealed a strong founder effect and a variable effect of geographic distance and climate on their population structures. Main Conclusions The high biodiversity and presence of potential specialised taxa highlight the conservation value of freshwater rock pools. While some tardigrade species may be able to easily disperse and have a large geographic range, other species show isolation by distance patterns and their genetic diversity may be negatively affected by habitat loss. Our results call for a bigger effort in identifying, mapping, characterising and protecting freshwater rock pools as underlooked but important habitats.