Brachionus calyciflorus is a species complex consisting of four recently described species. Although several lines of evidence support their species status, hybridization between two of the sibling species B. calyciflorus s.s. and B. elevatus has been inferred from both field and laboratory studies. In this study, we tested for the existence of prezygotic barriers between these species by performing two types of cross-fertilization experiments. In a ‘mate competition’ experiment we exposed mictic females to equal numbers of conspecific and allospecific males and demonstrate that intraspecific fertilizations occur at much higher frequencies than interspecific fertilizations, providing evidence for a strong prezygotic reproductive barrier. This result was consistent across numerous combinations of parental genotypes. In addition, by creating interspecific combinations of mictic females and males in a ‘no choice’ experiment, we found that interspecific fertilization success is independent of fertilization direction while it does seem to depend on maternal genotype. Our results demonstrate the existence of a strong prezygotic barrier that may play an important role in the maintenance of species boundaries. Yet, the observation of hybrids also shows a potential for gene flow between the species through hybridization.