A strongly divergent lineage, putatively a new cryptic species, of colonial ascidian was first detected as an anomalous sample in a population genomics study of the well-known worldwide invasive species Didemnum vexillum Kott, 2002. This putative new taxon, found in a marina in Roscoff, France, is indistinguishable from Didemnum vexillum in the external aspect and coexists with it in syntopy. However, morphological characters such as spicules and larvae allow a clear-cut distinction. In accordance with the preliminary results based on genome-wide analyses, morphological traits and mitochondrial sequences of the cytochrome oxidase I gene both support the establishment of a new species Didemnum pseudovexillum sp. nov. Previous unidentified sequences in public databases showed that the new species is also present in NW Mediterranean marinas. Didemnum pseudovexillum sp. nov. is assigned for the time being a cryptogenic species status, although its presently known disjoint distribution across two biogeographic regions and its presence in ports are suggestive of an introduced species. Further studies should be performed to ascertain its current distribution and putative natural range and settle its native vs. non-native status. This finding casts doubts on previous reports of Didemnum vexillum and also calls for caution when performing fast field surveys of non-indigenous species such as rapid assessment surveys (RAS) or BioBlitz surveys, based solely on external characters.