Background Developing effective conservation plans for multi-functional landscapes requires an accurate knowledge of the relative conservation value of different land-uses. A growing number of tropical ecologists have evaluated conservation value using the number (or proportion) of species that are unique to primary or old-growth forests. However, estimates of the conservation value of modified land-uses may be inflated by the presence of occasional species (e.g. singletons and doubletons) that may be unable to exist as viable populations in isolation. Methodology/Principal Findings We use a unique 15-taxa dataset from a mixed-use forest landscape in the Brazilian Amazon to test the hypothesis that the removal of occasional species from sample data can increase estimates of the value of primary forest for biodiversity conservation. Conclusions/Significance Estimates of conservation value that are based on the proportion of species that are unique to tropical primary or old-growth forests are highly sensitive to decisions researchers make regarding the inclusion or exclusion of occasional species. By removing singletons from modified forest samples, and considering only those species known to occur in primary forest, we almost double estimates of the conservation value of tropical primary forests.