Invasive species are an increasing threat to biological diversity as well as a leading cause of recent species’ extinctions. Invasives spread quickly and efficiently, and the U.S spends millions of dollars annually in the control and eradication of these species. More information is necessary in order to predict which species may become invasive. Rubus (Rosaceae) was chosen for study because this genus includes various ploidy levels, reproductive modes, and species that are invasive as well as native. Three Rubus species were chosen to represent apomictic and tetraploid invasives (Rubus armeniacus), a sexual and diploid native species (R. occidentalis), and a sexual and diploid invasive species (R. phoenicolasius). Specimens were collected across the U.S. and two different genetic fingerprinting techniques were used; Amplified Fragment Length Polymorphism (AFLP) and Randomly Amplified Fingerprints (RAF). Using three AFLP primers and two RAF primers, genetic similarity was determined and phylograms were constructed. Through statistical analysis and phylogram data it was determined that there might be slightly more genetic diversity in native R. occidentalis than in invasive R. phoenicolasius. Genetic diversity between apomictic and tetraploid Rubus armeniacus and the two sexual and diploid Rubus species were so similar that no distinction could be made, although the mean pairwise distances and mean number of alleles were significantly different. It was also found that geographic distance and genetic similarity do not appear to be related in these three Rubus species. During the course of this study it was also observed that the AFLP technique produced more alleles than the RAF technique, although this difference was not significant.