The Pontic shad (Alosa immaculata Bennett 1835) is an anadromous clupeid that grows to reproductive age in the Black Sea and migrates into the Danube via principal delta branches to spawn upstream. Spawning takes place at different times and different river kilometers, with most individuals spawning only once during their lifetime. The Pontic shad’s maximum migratory route, hence its range, was shortened to rkm 863 by the construction of the Iron Gates 2 dam (IG2) in 1984. Another dam is located farther upstream at rkm 943. Adults that migrate for spawning to IG2 traverse territorial waters of four different countries. Despite the species’ high commercial and cultural value, its population decline (listed as Vulnerable by IUCN) and disparate national fishing regulations, current knowledge of its life history, population structure and migratory behavior up the Danube remains surprisingly poor. To develop species-specific molecular tools and obtain a more detailed image of meta-population structure and the migratory behavior of sub-populations, from 2016 to 2018 we sampled in a variety of locations throughout spawning migration season. Preliminary population genetic analyses indicate that individuals reaching the IG2 dam are more closely related to those migrating up the northern branch of the delta, shared by Romania and Ukraine, than those migrating up the southern branch which is in Romania. Knowing more about the migration timing and routes of fish arriving at the IG2 dam can help guide decisions about the need for their passage at the dams and possible technical solutions. Currently, any effort to construct fish passes at the Iron Gates would require international collaboration and immense financial investment. Using existing navigation locks may be a solution, but more knowledge is needed about fish behavior at the dams. Environmental DNA sampling, to be developed on the basis of this research, is a promising tool.