Most landscape genetic studies assess the impact of landscape elements on species' dispersal and gene flow. Many of these studies perform their analysis on all possible population pairs in a study area and do not explicitly consider the effects of spatial scale and population network topology on their results. Here, we examined the effects of spatial scale and population network topology on the outcome of a landscape genetic analysis. Additionally, we tested whether the relevant spatial scale of landscape genetic analysis could be defined by population network topology or by isolation-by-distance (IBD) patterns. A data set of the wetland grasshopper Stethophyma grossum, collected in a fragmented agricultural landscape, was used to analyse population network topology, IBD patterns and dispersal habitats, using least-cost transect analysis. Landscape genetic analyses neglecting spatial scale and population network topology resulted in models with low fits, with which a most likely dispersal habitat could not be identified. In contrast, analyses considering spatial scale and population network topology resulted in high model fits by restricting landscape genetic analysis to smaller scales (0–3 km) and neighbouring populations, as represented by a Gabriel graph. These models also successfully identified a likely dispersal habitat of S. grossum. The above results suggest that spatial scale and potentially population network topology should be more explicitly considered in future landscape genetic analyses.