Invasions of nonindigenous pests constitute a growing threat to agriculture and ecosystems due to their potential for severe ecological and economic impacts. The number of individuals in an invading propagule can greatly influence the success of the invasion and has a large impact on the resulting population’s level of genetic diversity. Determining the propagule size can aid in the control of an outbreak by indicating the strength of the genetic bottleneck, the mode of introduction and whether the invasion was an isolated event or whether gene flow is continuous. Using a simulation method, seven different statistics were investigated for estimating the propagule size of an outbreak population. For outbreaks originating from populations with high genetic diversity, the number of alleles was a good estimator of propagule size. When, however, the genetic diversity of the source population was already reduced, allele frequency measures, particularly the likelihood of obtaining the outbreak population from the source population, gave more accurate estimates. In neither case was heterozygosity a good estimator of propagule size. Larger sample sizes from the outbreak population were needed to accurately estimate large propagule sizes. Applying this information to a fruit fly outbreak, it was found that just five flies were needed to found the major population in and around Alice Springs. This has led to a severe reduction in the number of alleles, particularly rare alleles in this population. The data strongly suggest that the population originated from a single founder event. As such this population would be ideal to target with the sterile insect technique in a bid to eradicate fruit fly from the area.