1. Beta diversity is a measure of the taxonomic differentiation between habitats/localities within an assemblage, and is normally calculated as a set of pairwise taxonomic “distances” between the localities. 2. Due to the incomplete sampling, beta diversity estimates for fossil assemblages will always be higher than the true value. However, the difference between the observed and true distances will vary greatly depending on differences in the shape of the relative abundance distribution. 3. Using simulations, it is shown that incomplete sampling of a homogenous fauna with more even relative abundances of taxa produces higher beta diversity than one with very few extremely common taxa. 4. A new procedure is proposed for calculating beta diversity in the fossil record, whereby the observed distances are compared to the distance obtained by randomly resampling a homogenous fauna with the same abundance distribution. This procedure is named Relative Abundance Corrected beta diversity (RAC beta diversity). Simulations indicate that this method outperforms raw beta diversity estimates, providing beta diversity estimates closer to the true values even when the assumptions of the method are violated. 5. This method is applied to an empirical dataset: Permian-Triassic tetrapods from the Karoo Supergroup of South Africa. Increased provincialism is found across the Permian-Triassic boundary in contrast to uncorrected beta diversity patterns.