The European anchovy, Engraulis encrasicolus, in the Bay of Biscay suffered a collapse in census population size (Nc) starting in 2002, from which it did not recover until 2010. The slow recovery raised concern over sustainability, potential reduction in adaptive potential, and vulnerability to local extirpation. Long- and short-term effective population size (Ne), Ne/Nc ratio, and other genetic parameters were estimated to evaluate demographic signals of population decline. A total of 349 neutral single-nucleotide polymorphisms (SNPs) were screened in 330 anchovy individuals from the Bay of Biscay distributed across a 20-year period. We show that Nc fluctuations have not significantly affected short-term Ne, and therefore, genetic diversity has remained stable throughout the recent collapse. This study illustrates that Ne estimates should be incorporated into management plans. Our results on short-term Ne suggested that the anchovy in the Bay of Biscay has not faced any recent severe threat of losing evolutionary potential due to genetic drift. However, differences between short- and long-term Ne estimates suggested that the Bay of Biscay anchovy population may be currently much smaller than in the historical past. © 2016, Springer-Verlag Berlin Heidelberg.