Riparian trees, especially relict trees, are attractive and important for research to understand both past and recent biogeographical and evolutionary processes. Our work is the first study to elucidate the genetic diversity and spatial genetic structure of the canopy-dominating riparian Pterocarya fraxinifolia (Juglandaceae) along two altitudinal gradients in different river systems of the Hyrcanian forest, which is one of the most important refugium of relict trees in Western Eurasia. Altitudinal gradients were chosen along two river systems at 100, 400 and 900 m a.s.l. Leaf samples were collected from 116 trees, and the genetic diversity was evaluated with eight SSR markers. Overall, 39 alleles were identified for all of the populations studied. The observed heterozygosity (Ho) varied from 0.79 to 0.87 (with a mean of 0.83). The results of the AMOVA analysis indicated that the variation within populations was 88%, whereas the variation among populations was 12% for all of the gradients. A structure analysis indicated that 93% of the trees were grouped in the same gradient. The genetic distance based on Fst confirmed the structure result and indicated a high rate of gene flow among the investigated populations. Based on high gene flow (low differentiation of the population along the same river) and the clearly distinct genetic structure of the investigated gradients, it can be concluded that rivers are the main seed dispersal vector among P. fraxinifolia populations. The genetic diversity of P. fraxinifolia did not show any trend from upstream to downstream. The high level of gene flow and uniform genetic diversity along each river suggest the “classical” metapopulation structure of the species.