Simulated data can be useful for planning molecular marker studies. The objective of this study was to test if the genotypic sampling scheme and marker system used to characterize the genetic structure of an invasive plant were sufficient to detect genetic structure given migration, population growth, and selection. Reed canarygrass (Phalaris arundinacea) is an important forage and ornamental crop, native to circumboreal regions. It is also a global invasive species with a complex demographic history. For the molecular study, 90 Inter Simple Sequence Repeat (ISSR) dominant markers were used to characterize the genetic structure of 76 European and North American populations. To model the effects of marker quantity, simulated data sets were generated using 20, 45, 90, or 150 markers. Sample size effects were modeled by varying the number of individuals sampled from each population from 1 to 20. To test the ability of the analyses to detect relevant biological phenomena, dominant markers were simulated under models of population growth, migration, and selection. Simulated data sets were analyzed using STRUCTURE and Analysis of Molecular Variance (AMOVA). The results of some preliminary analyses on the 90-marker data sets indicates that the sampling and marker systems used for the molecular data were sufficient to detect well-differentiated genetic groups, but that unequal sampling and increasing correlation in allele frequencies among regions can cause STRUCTURE to fail to detect all distinct groups.