Our studies of cottonwoods show that diverse species from microbes to vertebrates are sensitive to individual plant genotypes and that the application of genetics to restoration can have major impacts on biodiversity and the success of any restoration effort. Our studies have resulted in three major findings. 1. Genetic analyses of restoration sites and wild populations show that we are currently failing to mimic the genetic structure of natural stands in our restoration plantings. This may have negative community consequences. 2. Biodiversity is positively correlated with genetic diversity in cottonwoods. For example the genetic diversity in stands of cottonwoods explains about 60% of the variation in the diversity of an arthropod community composed of 207 arthropod species. Thus by altering genetic diversity of the trees used in restoration we may influence the diversity of insects and the organisms dependent upon them for survival (e.g. birds and mammals). 3. The use of local stock may not be the best for restoration. For example in a recent planting using 6000 Fremont cottonwoods derived from sites throughout their natural range we found that local genotypes suffered higher mortality in an initial selection event than genotypes derived from sources as far as 500 miles away. While we are not advocating a departure from using local stock it is important to consider that with increasing climate change and anthropogenic impacts which change the local environment (e.g. temperature salinity hydrology fragmentation) local stock may no longer be best adapted to the local environment.