Background: In the context of the increasing circulation of arboviruses, a simple, fast and reliable identification method for mosquitoes is needed. Geometric morphometrics have proven useful for mosquito classification and have been used around the world on known vectors such as Aedes albopictus. Morphometrics applied on French indigenous mosquitoes would prove useful in the case of autochthonous outbreaks of arboviral diseases. Methods: We applied geometric morphometric analysis on six indigenous and invasive species of the Aedes genus in order to evaluate its efficiency for mosquito classification. Results: Six species of Aedes mosquitoes (Ae. albopictus, Ae. cantans, Ae. cinereus, Ae. sticticus, Ae. japonicus and Ae. rusticus) were successfully differentiated with Canonical Variate Analysis of the Procrustes dataset of superimposed coordinates of 18 wing landmarks. Conclusions: Geometric morphometrics are effective tools for the rapid, inexpensive and reliable classification of at least six species of the Aedes genus in France.