Comparing available paleontological, archaeological, historical, and former distributional data with current natural history and distributions demonstrated a turnover in the French vertebrate fauna during the Holocene (subdivided into seven sub-periods). To this end, a network of 53 specialists gleaned information from more than 1300 documents, the majority never cited before in the academic literature. The designation of 699 species as native, vanished, or non-indigenous in France or in one or more of its biogeographical entities during the Holocene period was investigated. Among these 699 species, 585 were found to belong to one or more of these categories. Among the 154 species that fit the definition of non-indigenous, 86 species were new species for France during the Holocene. Fifty-one that were autochthonous vanished from France during this period. Among these 51 species, 10 (two birds and eight mammals) are now globally extinct. During the last 11 millennia, the turnover in the French vertebrate fauna yielded a net gain of 35 species. On a taxon-by-taxon basis, there was a gain in the sizes of the ichthyofauna (19 : 27%), the avifauna (10 : 3%) and the herpetofauna (7 : 9%) and a loss in the mammalian fauna (−1 : 1%). Values of a per-century invasion index were less than 1 between 9200 BC and 1600 AD but increased dramatically after this date. An exponential model fits the trajectory of this index well, reaching the value of 132 invasions per century for the last sub-period, which encompasses 1945–2002. Currently, the local ecological and economic impacts of populations of 116 species (75% of the 154 that satisfied the criteria for non-indigenous) are undocumented, and the non-indigenous populations of 107 vertebrate species (69%) are unmanaged. The delay in assessing the ecological and economical impact of non-indigenous species, which is related to a lack of interest of French academic scientists in the Science and Action programmes, prevents the public from becoming informed and hinders the debates needed to construct a global strategy. For such a strategy to be effective, it will have to be elaborated at a more global scale than in just France – definitely at least in Europe.