P-bodies are RNA-protein granules that form in the cytoplasm of eukaryotic cells in response to various stresses and are thought to serve as sites of degradation and/or storage of mRNAs. We recently discovered that P-bodies form in yeast in response to DNA replication stress induced by HU (hydroxyurea). P-body components are required for cell survival of replication stress as mutants lacking key P-body components Lsm1, Pat1 and Dhh1 are strongly sensitive to HU. Here, we aimed to identify mRNAs that are processed by P-bodies during replication stress. First, we performed a transcriptome study on lsm1∆ cells upon acute HU exposure to identify mRNAs that are stabilized in the absence of a functional P-body-dependent mRNA degradation pathway. Second, we used an SGA-based suppressor screen to identify genes whose expression is toxic in the absence of Lsm1 and Pat1 during replication stress. We found that the transcriptome in lsm1∆ is altered both during normal growth and during replication stress, with more than 800 mRNAs being stabilized in lsm1∆ compared to wild type. Interestingly, we found that inactivation of the coding sequence of 6 of those 800 mRNAs was able to suppress HU sensitivity of lsm1∆ and pat1∆ strains suggesting that these genes encode mRNAs that need to be degraded in a P-body dependent manner upon HU exposure. Among these, we identified YOX1, a gene encoding a transcription repressor critical for the regulation of cell cycle and DNA replication genes. Consistent with P-bodies regulating YOX1 mRNA abundance, we found that YOX1 mRNA localizes to P-bodies and accumulates at P-bodies in the absence of the mRNA exonuclease Xrn1. To gain insight into the role of Yox1 during replication stress, we identified 156 genes that are down-regulated upon YOX1 overexpression. Among this set of targets, we found that de-repression of ALD6, encoding a cytoplasmic acetaldehyde dehydrogenase, is critical for replication stress resistance. Indeed, accumulation of acetaldehyde, the substrate of Ald6, is strongly toxic for cells experiencing DNA replication stress. Together, our data suggest a model where YOX1 mRNA abundance is post-transcriptionally regulated by P-bodies in order to reduce the level of the Yox1 transcription repressor and therefore prevent repression of genes necessary for survival of DNA replication stress.