Neutral molecular markers are gene sequences where variants are considered to confer no fitness advantage, such as microsatellites and mitochondrial haplotypes. Several types of neutral marker are easy to develop, cheap to use, and have found extensive application for addressing ecological questions. In biocontrol, these markers are used to simplify identification of cryptic species and of prey remains in predators. Here, we address the potential of neutral molecular markers for determining the relative performance of a “superior” strain of a species after release into an already established conspecific population. We used modeling to show that only under very limited conditions can traditional neutral markers be used to demonstrate that beneficial genetic variation was successfully introgressed into the existing population. However, new population genomic methods do make it possible to track alleles at a large number of loci and consequently make it possible to show if alleles from a superior strain spread in an already established conspecific population.