Hybridization is known to occur in a wide range of avian species, yet the rate and persistence of hybridization on populations is often hard to assess. Genotyping using variable genetic marker sets has become a common tool to identify hybrid individuals, however assignment outputs can differ depending on the marker set used. Here, we study hybrid assignment in two sibling Hippolais warblers, where hybrid assignment has shown to differ between SSR and AFLP markers. Simulation of heterospecific individuals as well as backcrosses (typed using SSR markers) reveals a rapid loss of assignment probability in higher backcross generations. However, the characterization of F1 hybrids was clearly distinguished from both parental taxa. The differences in marker sets are not contradictory but complementary. The rate of hybridization is lower than previously expected with AFLP markers but introgression might be long-lasting. This could be either due to differences in power of the marker systems used or due to non-neutral variation covered by AFLP but not SSR markers. We call for more attention to be paid regarding the potential limits of classical marker systems to investigate hybridization and its persistence in natural systems.