Molecular surveys and studies of the muscle anatomy made evident that the mesopsammic gastrotrich Xenotrichula intermedia, previously regarded as a cosmopolitan species, comprises several distinct taxonomic units. These entities are to date referred to as cryptic species. Although other morphological traits seemed insufficient to differentiate geographically distant populations, investigations of the myomorphology displayed significant differences. Three muscular morphotypes of X. intermedia are known and distinguishable via properties of their dorsoventral and circular musculature. However, previous studies using confocal laser scanning microscopy (CLSM) conducted observations of the muscle architecture that aimed to apply older terminology of the only existing reconstruction that was based on fluorescence microscopy. Since detailed 3D reconstructions of the myoanatomy were never performed, comparisons between different morphotypes of X. intermedia stay a difficult endeavor. In this study, the muscular system of a North Sea population of X. intermedia is investigated and reconstructed using CLSM and 3D reconstruction software. Our aim is to test whether this population, adjacent to the type locality of X. intermedia, constitutes another muscular morphotype. The overall musculature of the North-Sea population is similar to that of the Mediterranean specimens. A Baltic Sea individual appears myoanatomically identical to these populations, too. This indicates a distinct morphotype with a pan-European distribution. Since the known muscular morphotypes are clearly distinguishable, we propose the presence of a species complex comprising a pan-European X. intermedia, a Persian X. aff. intermedia and a NW Atlantic X. aff. intermedia. Furthermore, our investigation demonstrates a much higher complexity of the longitudinal musculature than previously assumed, which leads us to reinterpret earlier myomorphological data, amend some terminology, and reconsider statements of homology that will provide a feasible foundation for future comparative studies.