Given the pending biodiversity crisis, species delimitation is a critically important task in conservation biology, but its efficacy based on single lines of evidence has been questioned as it may not accurately reflect species limits and relationships. Hence, the use of multiple lines of evidence has been portrayed as a means to overcome identification issues arising from gene/species tree discordance, morphological convergence or recent adaptive radiations. Here, the integrative taxonomic approach has been used to address the study of the Monocelis lineata species complex. The taxonomic resolution of the complex is challenging, as the species lacks sclerotised copulatory structures, which as a rule of thumb aid identification in Proseriata. Eighteen populations, which encompass most of the geographic range of the complex, were studied using morphology, karyology, crossbreeding experiments and molecular analysis. These different markers provided evidence of four (karyology) to eight (morphology) discrete entities, whereas crossings showed various degrees of intersterility among the tested populations. Molecular species delimitation revealed a different number of candidate species, spanning from five (ABGD and K/θ) to 11 (GMYC). Such incongruences reflect the multifaceted evolutionary history of M. lineata s.l. and hamper the full taxonomic resolution of the complex. However, two candidate species were consistently validated by all of the markers and are described as new species: Monocelis algicola nov. sp. and M. exquisita nov. sp. The latter species appear to have a restricted distribution, and the possibility that meiofaunal taxa may be of conservation concern is discussed.