Assessing the distribution of species in natural environments is essential for their use in environmental surveys. Here, we investigate the distribution of three pseudo-cryptic species formerly lumped in the morphospecies Ammonia tepida (Cushman, 1926), commonly found on estuarine mudflats along the European coasts: Ammonia veneta Schultze, 1854 (T1), Ammonia aberdoveyensis Haynes, 1973 (T2) and Ammonia confertitesta Zheng, 1978 (T6). We studied their distribution at 51 sites located in seven estuaries of the French North Atlantic coast (Elorn, Aulne, Odet, Crac'h, Auray, Vilaine, Vie), using both morphological and molecular identification methods. Ammonia veneta was detected by both approaches at most of the stations. While A. aberdoveyensis was frequently identified by the morphological method but not detected with metabarcoding, the presence of A. confertitesta in the eDNA data often contrasted with its absence in the morphological analysis. The absence of A. aberdoveyensis in eDNA of sites where it was identified morphologically could be the consequence of its relative scarcity, and eventually a patchy distribution. Concerning A. confertitesta, we hypothesise that these contradictory results can be explained by the supposedly invasive character of this species. Despite the widespread presence of A. confertitesta genetic material (including adults, juveniles and propagules), a mature population has not yet fully developed everywhere. The seven investigated estuaries seem to represent different stages of replacement of the autochthonous species A. veneta and A. aberdoveyensis by A. confertitesta. Our study demonstrates that the combination of visual observations and molecular approaches is ideal for monitoring the progressive spreading of exotic species.