Conservation translocation breeding programmes often rely on neutral diversity as a measure of genetic ‘health’. However, incorporation of functional diversity, such as immune gene diversity, may better inform management decisions. Endemic to Aotearoa New Zealand, the Endangered tchūriwat' | tūturuatu | shore plover (Thinornis novaeseelandiae) is a species whose recovery may be hampered by a lack of immune gene diversity. Unlike birds in the wild, captive birds are highly susceptible to avian pox infections and show poor immune response to vaccination. Our previous research showed that, despite low toll-like receptor (TLR) gene diversity overall, wild and captive tchūriwat’ form two distinct genetic clusters. TLRs are a key part of recognition and activation pathways in the immune system. Here, we extend this research to characterise TLR gene diversity in relation to avian pox severity in the captive population before and after augmentation with birds from the wild. In addition to informing future augmentation strategies to improve disease outcomes for tchūriwat’, our approach for characterising TLR gene diversity is broadly applicable to conservation translocation breeding programmes for threatened birds in Aotearoa New Zealand and beyond.