Genetic diversity is important for the maintenance of the viability and the evolutionary or adaptive potential of populations and species. However, there are two principal types of genetic diversity: adaptive and neutral - a fact widely neglected by non-specialists. We introduce these two types of genetic diversity and critically point to their potential uses and misuses in population or landscape genetic studies. First, most molecular-genetic laboratory techniques analyse neutral genetic variation. This means that the gene variants detected do not have any direct effect on fitness. This type of genetic variation is thus selectively neutral and tells us nothing about the adaptive or evolutionary potential of a population or a species. Nevertheless, neutral genetic markers have great potential for investigating processes such as gene flow, migration or dispersal. Hence, they allow us to empirically test the functional relevance of spatial indices such as connectivity used in landscape ecology. Second, adaptive genetic variation, i.e. genetic variation under natural selection, is analysed in quantitative genetic experiments under controlled and uniform environmental conditions. Unfortunately, the genetic variation (i.e. heritability) and population differentiation at quantitative, adaptive traits is not directly linked with neutral genetic diversity or differentiation. Thus, neutral genetic data cannot serve as a surrogate of adaptive genetic data. In summary, neutral genetic diversity is well suited for the study of processes within landscapes such as gene flow, while the evolutionary or adaptive potential of populations or species has to be assessed in quantitative genetic experiments. Landscape ecologists have to mind these differences between neutral and adaptive genetic variation when interpreting the results of landscape genetic studies.