© 2022 Botanical Society of Scotland and Taylor & Francis.Background: Salix alba is a pioneer species of river ecosystems throughout Turkey. Its genetic diversity and population structure across these ecosystems is currently unknown. Aims: We investigated genetic diversity in Turkish S. alba to assess factors likely to shape the genetic structure of the species and to assist with conservation recommendations. Methods: Six hundred and forty-six individuals from 10 major river systems in Turkey were genotyped using 15 microsatellite markers. Between one and five sub-populations were sampled from each river system with 23 sub-populations sampled in total. Results: Populations contained moderately high levels of genetic diversity. Five genetic groups were detected by Bayesian clustering, with samples from particular river systems mainly assigned to particular genetic groups. This revealed a geographic structure, also detected by principal coordinate analysis, showing that particular river system populations in different parts of Turkey were genetically similar to each other but different from those in other parts of the country. Conclusion: Genetic isolation caused by geographic distance (in part) and natural barriers among river systems appear to have shaped the genetic structure of populations. The results have important implications for the conservation of genetic resources within S. alba and restoration of degraded Turkish populations of the species.