The incorporation of molecular data into current taxonomic practise has unravelled instances of incongruence among different data sets. Here we report a case of mitochondrial discordance in cobweb spiders of the genus Theridion Walckenaer, 1805 from the Iberian Peninsula. Morphological examination of samples from a country-wide bioinventory initiative revealed the existence of a putative new species and two nominal species belonging to the Theridion melanurum species group. The morphological delineation was supported by the molecular analysis of a nuclear marker but was at odds with the groups circumscribed by a mitochondrial marker. The causes of this discordance remained uncertain, once sample and sequencing errors and the existence of pseudogenes were discarded. The full sorting observed in the alleles of the more slowly evolving nuclear marker ruled out incomplete lineage sorting, while the geographic patterns recovered were difficult to reconciliate with ongoing hybridization. We propose that the apparent incongruence observed is most likely the result of old introgression events in a group with high dispersal abilities. We further speculate that endosymbiont-driven cytoplasmatic incompatibility could be involved in the fixation of mitochondrial haplotypes across species barriers. Additionally, we describe the new species T. promiscuumsp. nov., based on the presence of diagnostic morphological traits, backed up by the nuclear data delimitation. Our study contributes yet another example of the perils of relying on single methods or data sources to summarise the variation generated by multiple processes acting through thousands of years of evolution and supports the key role of biological inventories in improving our knowledge of invertebrate biodiversity.