Genotypic diversity of dominant species has been shown to have important consequences for community and ecosystem processes at a fine spatial scale. We examined the fine-scale (i.e., plant neighborhood scale, <1 m²) genotypic structure of Andropogon gerardii, a dominant species in the tallgrass prairie, which is a productive and endangered grassland ecosystem, employing the commonly used amplified fragment length polymorphism (AFLP) technique. In this paper we used two methods to assess the fine-scale genetic spatial structure of a dominant perennial grass, (1) we determined how many tillers to sample in a 1 m² area and (2) we developed AFLP markers that would differentiate between genotypes. By determining appropriate sampling and molecular techniques, our findings can be applied to questions addressing how genetic diversity of dominant species affect ecosystem processes in the tallgrass prairie.