Recent global efforts in biodiversity accounting, such as those undertaken through the Convention on Biological Diversity (CBD) and Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), are vital if we are to track conservation progress, ensure that we can address the challenges of global change, and develop powerful and scientifically sound indicators. Schlaepfer [1] proposes that we should work toward inventories of biodiversity that account for native and non-native species regardless of species origin and ecological context. We strongly disagree with the approach of combining counts of native and non-native species because this will reduce our capacity to detect the effects of non-native species on native biodiversity with potentially devastating consequences. Compelling and abundant evidence demonstrates that some non-native species can become invasive and produce major ecosystem disruptions and even native species extinction. Unfortunately, we still cannot be certain which non-native species will be the most detrimental (e.g., [2]). Combining native and non-native species together into a single biodiversity index would not only inflate biodiversity estimates and risk promoting the spread of invasive non-native species but would also ignore the fundamental ecological differences between the two groups. The critical differences that should be considered when assessing biodiversity include the following.