Brachionus calyciflorus is a recently described monogonont rotifer species complex that comprises four species. The observation of hybridisation between two of these species challenges this species delimitation. The mechanisms of reproductive isolation essential to the maintenance of species integrity remain unclear. Here, we conducted upscaled hybridisation experiments to obtain large numbers of hybrid and non-hybrid dormant propagules. Through hatching assays, we compared the zygote viability of hybrid with non-hybrid dormant propagules. Furthermore, we investigated populations of F1 hybrid clones and assessed their clonal growth rate and the ability to reproduce sexually. Our results demonstrated higher rates of morphological abnormality and associated mortality in dormant propagules of hybrids compared to non-hybrids yet hatching rates of healthy-looking propagules proved similar. F1 hybrids exhibited high clonal population growth rates, nevertheless, we also observed strong differences between clones and a strong influence of parental genotype identity. Two-thirds of the F1 hybrid clones showed a low incidence of sexual reproduction and almost never produced dormant propagules. Clones with high population growth rates seemed to invest less in sexual reproduction. Our results clearly demonstrate the existence of intrinsic postzygotic barriers caused by relatively high mortality of dormant propagules. Furthermore, the low ability of most hybrid clones to engage in sexual reproduction may reduce the long-term fitness of hybrid clones. These postzygotic barriers probably impede genetic exchange between parental species and contribute to the maintenance of their integrity.