Ecological study plots are usually treated as if they are flat. This does not hold for many situations such as mountains where topography is complex. In areas with complex topography individual relationships are not only determined by projection distance, but also by surface distance. To demonstrate this we compared projection and surface distances by analyzing spatial genetic autocorrelation for Castanopsis chinensis in two subplots (A and B) in the Dinghushan (DHS) national nature reserve in subtropical South China. We observed that the two types of distances generally result in similar fine-scale spatial genetic structure (SGS) patterning for the spatially less structured subplot B, but not for the highly structured subplot A. The present study shows clearly that accounting for plot architecture in plant species on topographically complex areas enables a more accurate picture of the underlying spatial genetic structure to emerge.