1. Although vertebrates have been reported to gain higher reproductive outputs by choosing mates, few studies have been conducted on threatened species. However, species recovery should benefit if natural mate choice could improve reproductive output (i.e., pair performance related to offspring number, such as increased clutch size, numbers of fertilized egg and fledglings). We assessed the evidence for major histocompatibility complex (MHC)-based mate preference in the endangered crested ibis (Nipponia nippon), and quantified the impacts of such choice on reproductive output. 2. We tested the hypothesis that crested ibis advertise “good genes” through external traits, by testing whether nuptial plumage characteristics and body morphology mediate mate choice for underlying genetic MHC variation. 3. We found differences between males and females in preferred MHC genotypes, external traits used in mate choice, and contributions to reproductive outputs. Females preferred MHC-heterozygous males, which had darker [i.e., lower total reflectance and ultraviolet (UV) reflectance] nuptial plumage. Males preferred females lacking the DABd allele at the MHC classⅡDAB locus, which had higher average body mass. DABd-free females yielded heavier eggs and more fledglings, while MHC-heterozygous males contributed to more fertilized eggs and fledglings. Fledging rate was highest when both parents had the preferred MHC genotypes (i.e., MHC-heterozygous father and DABd-free mother). Comparisons showed that free-mating wild and seminatural pairs yielded more fertilized eggs and more fledglings, with a higher fledging rate, than captive pairs matched artificially based on pedigree. 4. Conservation programs seldom apply modern research results to population management, which could hinder recovery of threatened species. Our results show that mate choice can play an important role in improving reproductive output, with an example in which an endangered bird selects mates using UV visual capability. Despite the undoubted importance of pedigree-based matching of mates in conservation programs, we show that free-mating can be a better alternative strategy.