The origin of the Antarctic continental extant fauna is a highly debated topic, complicated by the paucity of organisms for which we have clear biogeographic distributions and understanding of their evolutionary timescale. To shed new light on this topic, we coupled molecular clock analyses with biogeographic studies on the heterotardigrade genus Mopsechiniscus. This taxon includes species with endemic distributions in Antarctica and other regions of the southern hemisphere. Molecular dating using different models and calibration priors retrieved similar divergence time for the split between the Antarctic and South American Mopsechiniscus lineages (32–48 Mya) and the estimated age of the Drake Passage opening that led to the separation of Antarctica and South America. Our divergence estimates are congruent with other independent studies in dating Gondwanan geological events. Although different analyses retrieved similar results for the internal relationships within the Heterotardigrada, our results indicated that the molecular dating of tardigrades using genes coding for ribosomal RNA (18S and 28S rDNA) is a complex task, revealed by a very wide range of posterior density and a relative difficulty in discriminating between competing models. Overall, our study indicates that Mopsechiniscus is an ancient genus with a clear Gondwanan distribution, in which speciation was probably directed by a co-occurrence of vicariance and glacial events.