Australian state and federal agencies use a broad range of methods for sett
ing conservation priorities for species at risk. Some of these are based on
rule sets developed by the International Union for the Conservation of Nat
ure, while others use point scoring protocols to assess threat. All of them
ignore uncertainty in the data. In this study, we assessed the conservatio
n status of 29 threatened vascular plants from Tasmania and New South Wales
using a variety of methods including point scoring and rule-based approach
es. In addition, several methods for dealing with uncertainty in the data w
ere applied to each of the priority-setting schemes. The results indicate t
hat the choice of a protocol for setting priorities and the choice of the w
ay in which uncertainty is treated may make important differences to the re
sulting assessments of risk. The choice among methods needs to be rationali
zed within the management context in which it is to be applied. These metho
ds are not a substitute for more formal risk assessment.