A pattern of population structure called isolation-by-environment (IBE) evolves when gene flow connecting populations in different habitats is lower than expected. Although IBE is widespread, there is limited information on its magnitude compared with other factors influencing gene flow. We estimated the relative importance of IBE in the frog Rana temporaria in the Swiss Alps, a geographic context in which IBE should be relatively pronounced. The environmental factor potentially causing IBE was the length of the growing season, which is highly correlated with elevation. A sample of 992 individuals from 82 breeding sites were genotyped at 1827 single-nucleotide polymorphism markers; gene flow was estimated in four ways related to FST, genetic distance, allele sharing, and distance on a population graph. Gravity modeling and random forest regression evaluated the importance of six at-site covariates, 10 between-site covariates, and geographic distance. There was broad agreement among analysis methods and measures of gene flow: isolation-by-distance (IBD) and habitat quality between sites were of highest importance, the elevation and ruggedness of the dispersal path were about half as important, and IBE was about 10–20% as important as IBD. These results combine with other evidence to suggest that population divergence across elevational gradients is underway in amphibians.