Lactococcus lactis is a commonly used starter culture bacterium in cheese making and therefore experiences a number of different stressors (e.g. heat, osmotic, acid) affecting cell growth and survival. In previous work we found that high temperature incubation of Lactococcus leads to the formation of spontaneous mutations in the gdpP gene which leads to heat resistance and in some cases salt hypersensitivity. The gdpP gene (also known as yybT and llmg_1816) encodes a membrane bound protein cyclic-di-AMP (c-di-AMP) phosphodiesterase and therefore down-regulates the level of the stress signaling molecule c-di-AMP. In other Gram-positive bacteria (Bacillus subtilis, Staphylococcus aureus and Listeria monocytogenes) c-di-AMP has recently been found to play a role in cell wall homeostasis, β-lactam antibiotic resistance, biofilm formation, acid stress resistance, cell size and mammalian cell immune responses. In a screen for salt resistant suppressors of the Lactococcus gdpP mutant, we found destructive mutations in the dacA gene (llmg_0448), encoding the membrane bound c-di-AMP synthase, were very common. Over 40 independent nonsynonymous mutations, frameshift mutations or DNA insertions in the dacA gene were identified. Nonsynonymous mutations were found in and near the three predicted N-terminal transmembrane helices and also in the enzymatic domain. Levels of c-di-AMP in the gdpP mutant were significantly higher than the gdpP/dacA suppressor double mutants but were undetectable in wild-type. Autolysis of the gdpP mutant was slower than wild-type while the gdpP/dacA mutant autolysed faster, indicating changes in cell wall structure. From our results it can be concluded that the GdpP and DacA proteins regulate levels of the signaling molecule c-di-AMP which in turn regulates salt resistance in Lactococcus. These mutants obtained by non-GM approaches may be tenable for use in the fermentation industry.