RNA editing is a mechanism that alters the nucleotide sequence of transcripts; edited transcripts are thus different from what is encoded in the genome. If the edits occur in coding regions, non-synonymous changes will generate additional protein diversity. Environmental stress is one of the many triggers for RNA editing, and evidence for its role in stress response is emerging. Here, we identified nuclear-encoded genes undergoing RNA editing in S. microadriaticum, a dinoflagellate symbiont of reef-building corals. When subjected to several common environmental stressors, the editing frequencies of some genes shifted in a consistent pattern that was specific to the applied stress. Within these genes, the predicted edits were predominantly non-synonymous in nature, suggesting that RNA editing is introducing genotypic variability beyond the organism’s haploid genome, extending its capability to respond to stress. Our data suggest that differential RNA editing is a process that contributes to the capacity of these algal symbionts to acclimate to environmental stress.