The conservation of highly mobile species, such as black-cockatoos (Calyptorhynchus spp.), presents challenges for the agencies responsible for their management. Very few ecosystems and/or habitat remain that haven’t been affected by anthropogenic activity. More often than not, this results in species decline, but there are exceptions. Since European settlement, a large portion of the southwest corner of Western Australia has been cleared and modified for agriculture (~95,800 km2). Here we present the molecular toolkit used to investigate; (1) the relationship of cockatoos; (2) fragmented habitat and the resulting consequences of genetic diversity for the endangered white-tailed black-cockatoo; (3) deterrents for illegal trade and poaching; (4) preservation and augmentation of significant nesting habitat; and (5) adaption of dietary choices in today’s modified ecosystems. When the genetic data is combined, it provides another approach to understand species and ecosystem management in an ever-changing landscape.