AbstractThe fairy shrimpBranchinectella media, because of its passive dispersal capacity and scarce and irregularly distributed habitats (temporary saline aquatic systems), is an intriguing organism from a population genomics and conservation perspective. Stochasticity of dispersal events and the irregular distribution of its habitat might lead to low levels of population connectivity and genetic diversity, and consequently, populations with limited persistence through time. Indeed, by using genomic data (SNPs), we found a strong genetic structure among some of the geographically isolated Iberian populations ofB. media.Interestingly, we also obtained high estimates of effective population sizes. Lack of suitable habitat between populations (absence of a “stepping stone” network) and strong genetic differentiation suggest limited dispersal success inB. media. However, the high effective population sizes observed ensure persistence ofB. mediapopulations against genetic stochasticity (genetic drift). These results indicate that rescue-effect might not be essential for population persistence if they maintain high effective population sizes able to hold adequate levels of genetic diversity. Should high population sizes be reported in other low dispersing Anostraca, one might be optimistic with regard to their conservation status and fate, provided that their natural habitats remain undisturbed.