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Abstract Despite the importance of effective population size (Ne) in evolutionary and conservation biology, it remains unclear what factors have an impact on this quantity. The Nearly Neutral Theory of Molecular Evolution predicts a faster accumulation of deleterious mutations (and thus a higher dN/dS ratio) in populations with small Ne; thus, measuring dN/dS ratios in different groups/species can provide insight into their Ne. Here, we used an exome data set of 1,550 loci from 45 species of marsupials representing 18 of the 22 extant families, to estimate dN/dS ratios across the different branches and families of the marsupial phylogeny. We found a considerable heterogeneity in dN/dS ratios among families and species, which suggests significant differences in their Ne. Furthermore, our multivariate analyses of several life-history traits showed that dN/dS ratios (and thus Ne) are affected by body weight, body length, and weaning age.