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A methodology for partitioning of biodiversity into α, β and γ components has long been debated, resulting in different mathematical frameworks. Recently, use of the Rao quadratic entropy index has been advocated since it allows comparison of various facets of diversity (e.g. taxonomic, phylogenetic and functional) within the same mathematical framework. However, if not well implemented, the Rao index can easily yield biologically meaningless results and lead into a mathematical labyrinth. As a practical guideline for ecologists, we present a critical synthesis of diverging implementations of the index in the recent literature and a new extension of the index for measuring β‐diversity. First, we detail correct computation of the index that needs to be applied in order not to obtain negative β‐diversity values, which are ecologically unacceptable, and elucidate the main approaches to calculate the Rao quadratic entropy …