Aplacophorans are small, worm-like molluscs that lack a shell but possess calcareous sclerites instead. About 400 species have been described to date but there are likely many more that have yet to be discovered. Moreover, some known species may represent “cryptic species,” which are morphologically identical, but different genetically. Wirenia argentea is an emerging model organism in aplacophoran research that is easily collected and can be spawned in the lab. However, previous work revealed at least one cryptic species that may co-occur with Wirenia argentea, raising concern that our experiments might be conducted on two or more genetically distinct species. In order to characterize the diversity and evolution of Wirenia in the Northeastern Atlantic, we imaged specimens collected during the IceAGE cruises using stereo light microscopy and selected a subset of specimens from throughout the Northeast Atlantic for high-resolution imaging using scanning electron microscopy (SEM). From there, we extracted high-quality DNA from the same specimens and sequenced fragments of the mitochondrial 16S and COI genes and the nuclear H3 gene. Maximum likelihood and species delimitation analyses reveal that there are 7-24 different species, depending on the approach used, compared to the two species described in the genus to date. Because SEM data were collected for every specimen, we were able to re-examine our morphological data and identify characters that help us identify at least some of these “cryptic” species. By knowing which species of Aplacophora live in which regions of the ocean and the species’ biodiversity, it allows for more targeted access in future experiments and helps ensure that cryptic, co-occurring species are not being inadvertently compared in experiments.