Among benthic foraminifera, the genus Ammonia is characterized by high morphological variability which makes it particularly challenging to recognize using traditional morphology-based taxonomy. Despite the joint efforts made by both molecular and morphological taxonomists, it is still hard to identify different phylotypes based on their morphology. A new method was developed recently to discriminate three NE Atlantic phylotypes of Ammonia (T1, T2, and T6). This method is based on two morphometrical parameters using scanning electron microscope (SEM) images (i.e., the average pore diameter and the elevation of sutures on the spiral side), resulting individuals being correctly assigned to their phylotype in more than 90% of cases. In this study, we assess the possibility of implementing these criteria using a stereomicroscope. Phylotype assignations by SEM and stereomicroscopic identifications are in accordance for 62.6% of the scrutinized foraminifera and increase up to 79.5% when only the phylotype T6 is considered. Though the stereomicroscopic identification of Ammonia phylotypes based on these two morphological parameters needs to be cross-validated using molecular tools, this approach noticeably allows the identification of an individual 3 to 7 times faster than using a SEM. The ratio between accuracy and efficiency, an issue that is also attributable to the use of the rose Bengal staining method, suggests prioritizing the use of stereomicroscope identifications in large foraminiferal surveys. Finally, in the context that Ammonia phylotype T6 potentially being an alien species in Europe, this method will help to quickly identify Ammonia phylotypes; hence contributing to monitor the presence of T6 in different regions and then, offering interesting research perspectives to assess the timing and/or the progression of the possible invasion.