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Genetic diversity is a key part of biodiversity, threatened by human activities that lead to loss of gene flow and reduction of effective population sizes. Gene flow is a result of both landscape connectivity and demographic processes determining the number of dispersing individuals in space and time. Thus, the effect of human impact on processes determining the level of genetic diversity must be interpreted in the context of basic ecological conditions affecting survival and recruitment. When the intensity of human impact and habitat suitability correlate, the effect on genetic diversity and gene flow may be challenging to predict. We compared genetic diversity, gene flow and landscape resistance in two contrasting landscapes in Norway for the pond‐breeding amphibian Triturus cristatus: a highly human‐impacted, agricultural landscape with ecologically productive habitats, and a forested landscape with less productive habitats and lower levels of human impact. Our results show that genetic diversity was higher and gene flow lower within the forested landscape. Microclimatic moisture conditions and vegetation cover were important determinants of landscape resistance to gene flow within both landscapes. There were indications that landscape resistance was increased by minor roads in the forested landscape, which was not the case for the agricultural landscape, suggesting a higher vulnerability to human interference within the landscape matrix for the populations in less productive habitats. Our findings suggest that the effect of human impact on genetic diversity may not be straightforward but modulated by the ecological conditions underlying local demographic processes. Populations within both landscapes seem to be vulnerable to loss of genetic diversity, but due to different mechanisms. This has implications for the choice of relevant management actions, that is, increasing population stability may be more relevant within an agricultural landscape still permeable for dispersal, while conserving dispersal corridors may be more appropriate in the forested landscape, to avoid isolation and increased genetic drift. [ABSTRACT FROM AUTHOR]