Aquatic faunas in fresh, brackish, and salt waters are usually well defined and differ amongst these three habitats. Nonetheless, some animals are known to be euryhaline, namely present across wide salinity ranges. The wide tolerance of putative euryhaline species has, however been refuted in some cases by DNA taxonomy, which has uncovered cryptic diversity with narrow ecological niches. We aim to improve knowledge on the putative euryhalinism of microinvertebrates and test whether it might actually be a real phenomenon or if euryhaline species are mostly a consequence of our previous inability to identify cryptic species with narrow salinity ranges, as discovered in Brachionus plicatilis. Using morphological analyses and DNA taxonomy, we investigated the species reality and distribution of a putative euryhaline rotifer species, Testudinella clypeata, and evaluated whether cryptic species are ecologically and/or geographically segregated. Different DNA taxonomy approaches concurred in revealing the presence of seven cryptic species within the T. clypeata morphospecies, which, in contrast to what has been previously detected, are actually euryhaline. Moreover, differences in analysed morphological traits were not significantly different amongst cryptic species. This suggests that DNA taxonomy improves our estimates of the actual diversity of microscopic species, in contrast to the morphological approach.