In today’s environmental crisis, conservationists are increasingly confronted with terminally
endangered species whose last few surviving populations may be afected by allelic introgression from
closely related species. Yet there is a worrying lack of evidence-based recommendations and solutions
for this emerging problem. We analyzed genome-wide DNA markers and plumage variability in a
critically endangered insular songbird, the Black-winged Myna (BWM, Acridotheres melanopterus).
This species is highly threatened by the illegal wildlife trade, with its wild population numbering in the
low hundreds, and its continued survival urgently depending on ex-situ breeding. Its three subspecies
occur along a geographic gradient of melanism and are variably interpreted as three species.
However, our integrative approach revealed that melanism poorly relects the pattern of limited
genomic diferentiation across BWM subspecies. We also uncovered allelic introgression into the
most melanistic subspecies, tertius, from the all-black congeneric Javan Myna (A. javanicus), which is
native to the same islands. Based on our results, we recommend the establishment of three separate
breeding programs to maintain subspeciic traits that may confer local adaptation, but with the option
of occasional cross-breeding between insurance populations in order to boost genetic diversity and
increase overall viability prospects of each breeding program. Our results underscore the importance
of evidence-based integrative approaches when determining appropriate conservation units. Given
the rapid increase of terminally endangered organisms in need of ex-situ conservation, this study
provides an important blueprint for similar programs dealing with phenotypically variable species.