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The evolutionary processes that drive variation in genome size across the tree of life remain unresolved. Effective population size (N e) is thought to play an important role in shaping genome size [ 1–3 ]—a key example being the reduced genomes of insect endosymbionts, which undergo population bottlenecks during transmission [ 4 ]. However, the existence of reduced genomes in marine and terrestrial prokaryote species with large N e indicate that genome reduction is influenced by multiple processes [ 3 ]. One candidate process is enhanced mutation rate, which can increase adaptive capacity but can also promote gene loss. To investigate evolutionary forces associated with prokaryotic genome reduction, we performed molecular evolutionary and phylogenomic analyses of nine lineages from five bacterial and archaeal phyla. We found that gene-loss rate strongly correlated with synonymous substitution rate (a proxy for mutation rate) in seven of the nine lineages. However, gene-loss rate showed weak or no correlation with the ratio of nonsynonymous/synonymous substitution rate (d N / d S). These results indicate that genome reduction is largely associated with increased mutation rate, while the association between gene loss and changes in N e is less well defined. Lineages with relatively high d S and d N , as well as smaller genomes, lacked multiple DNA repair genes, providing a proximate cause for increased mutation rates. Our findings suggest that similar mechanisms drive genome reduction in both intracellular and free-living prokaryotes, with implications for developing a comprehensive theory of prokaryote genome size evolution. • Mutation rate is correlated with gene loss in multiple prokaryotic lineages • Changes in effective population size are weakly associated with gene loss • Increased mutation rates should be considered in theories of genome-size evolution Using phylogenomic analyses, Bourguignon et al. show gene loss and DNA substitution rates (d N , d S) are correlated in seven of nine prokaryote lineages examined. In contrast, gene loss rate is weakly associated with d N / d S. These results indicate that mutation rate, rather than effective population size, is a key driver of genome reduction in prokaryotes. [ABSTRACT FROM AUTHOR]