24Missing data and genotyping errors are common in microsatellite data sets. We used 25 simulated data to quantify the effect of these data aberrations on the accuracy of population 26 structure inference. Data sets with complex, randomly-generated, population histories were 27 simulated under the coalescent. Models describing the characteristic patterns of missing data and 28 genotyping error in real microsatellite data sets were used to modify the simulated data sets. 29Accuracy of ordination, tree-based, and model-based methods of inference was evaluated before 30 and after data set modifications. The ability to recover correct population clusters decreased as 31 missing data increased. The rate of decrease was similar among analytical procedures, thus no 32 single analytical approach was preferable. For every 1% of a data matrix that contained missing 33 genotypes, 2-4% fewer correct clusters were found. For every 1% of a matrix that contained 34 erroneous genotypes, 1-2% fewer correct clusters were found using ordination and tree-based