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Abstract Single-stranded RNA molecules can form intramolecular bonds between nucleotides to create secondary structures. These structures can have phenotypic effects, meaning mutations that alter secondary structure may be subject to natural selection. Here, we examined the population genetics of these mutations within Arabidopsis thaliana genes. We began by identifying derived SNPs with the potential to alter secondary structures within coding regions, using a combination of computational prediction and empirical data analysis. We identified 8,469 such polymorphisms, representing a small portion (∼0.024%) of sites within transcribed genes. We examined nucleotide diversity and allele frequencies of these “pair-changing mutations” (pcM) in 1,001 A. thaliana genomes. The pcM SNPs at synonymous sites had a 13.4% reduction in nucleotide diversity relative to non-pcM SNPs at synonymous sites and were found at lower allele frequencies. We used demographic modeling to estimate selection coefficients, finding selection against pcMs in 5′ and 3′ untranslated regions. Previous work has shown that some pcMs affect gene expression in a temperature-dependent matter. We explored associations on a genome-wide scale, finding that pcMs existed at higher population frequencies in colder environments, but so did non-PCM alleles. Derived pcM mutations had a small but significant relationship with gene expression; transcript abundance for pcM-containing alleles had an average reduction in expression of ∼4% relative to alleles with conserved ancestral secondary structure. Overall, we document selection against derived pcMs in untranslated regions but find limited evidence for selection against derived pcMs at synonymous sites.