In the past decade much attention has focused on the role that genetics can
play in the formation of management strategies in conservation. Here, we d
escribe genetic diversity in the world's largest lizard, the Komodo dragon
(Varanus komodoensis), examining the evolutionary relationships and populat
ion genetic history of the four islands in south-east Indonesia, which form
the vast majority of its range. We identify distinct genetic groups for co
nservation. The population on the island of Komodo shows by far the largest
values of genetic divergence and is proposed that it should be a separate
conservation management unit. Other populations, surviving either on small
islands with substantially reduced genetic variability, or in isolated patc
hes, are identified as particularly vulnerable to stochastic threats and ha
bitat loss. Our results provide an example of how data defining intraspecif
ic levels of genetic divergence can provide information to help management
plans, ensure the maintenance of genetic variability across populations and
identify evolutionary potential within endangered species.