Freshwater systems are one of the environments most impacted by human activity, with pollution being a highly important factor. In Chile, several rivers exhibit varied levels of pollution, one of which is the Maipo River basin where the city of Santiago is located. The silverside Basilichthys microlepidotus (Jenyns) is an endemic fish species that inhabits this basin, thus we hypothesized that pollution has affected gene diversity and migration in populations of B. microlepidotus from the Maipo River basin. The aim of this study was to identify the population structure of B. microlepidotus in this basin and to determine if the populations of the silverside inhabiting polluted sites present differences in gene diversity and gene flow compared to populations inhabiting non‐polluted areas. Using the variability of eight microsatellites, five populations of silverside were detected; three inhabiting non‐polluted sites and two inhabiting polluted sites. From this, it was inferred that B. microlepidotus has been able to tolerate pollution in the Maipo River basin. No differences in gene diversity or migration were detected between polluted and non‐polluted sites but comparison with historical estimation revealed an increase in the current migration rate when all the data from the basin were compared. A reduction in current effective population size was also observed when compared to historical values, and this is probably due to river degradation. Despite the disappearance of other fish species recorded at this basin, our results suggest that B. microepidotus is tolerant to pollution, thus indicating that native species respond differently to this environmental factor.

1. The presence of a dam disturbs river flow, which in turn directly affects the communities and evolutionary potential of riverine species. To detect the ecological effects of a dam on genetic diversity, genetic structure, and their progress in time, two riverine fishes living upstream and downstream of an irrigation reservoir were studied at two periods after its construction in 2004 in central Chile. 2. Samples of the Neotropical silverside Basilichthys microlepidotus and the pencil catfish Trichomycterus areolatus were obtained 2 and 7 years after the Corrales Dam was built. The microsatellite DNA variability of both species upstream and downstream of the dam was analysed. 3. Fish analysed 2 years after dam construction did not show genetic differences between upstream and downstream populations; however, fish obtained 7 years after dam construction showed differences between populations above and below the dam and differences from individuals collected 5 years earlier. 4. The current effective population sizes of both species were smaller in samples obtained upstream than in samples obtained downstream. Simulations showed a migration equal to zero as most probable after reservoir construction, suggesting that the dam is an impermeable barrier to the movement of individuals of these species. These results showed that population fragmentation in time could be related to the barrier imposed by the dam. 5. In a scenario of no new contact between populations located upstream and downstream of the dam, the simulation predicts a reduction of genetic diversity ranging from 3.98 to 8.09% over the next 60 years. 6. Analyses suggest that the Corrales Reservoir may be affecting the evolutionary potential of the populations upstream and downstream from the dam.

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