SAGA (Spt-Ada-Gcn5 acetyltransferase) is a highly conserved protein complex in eukaryotes, which plays a role in many important cellular processes, including transcriptional activation and mRNA exportation. In order to investigate the potential biological function of SAGA subunit, we performed a yeast two-hybrid screen using a core structural subunit of SAGA in fission yeast, Spt20, as the bait. Ppbl, catalytic subunit of calcineruin was identified in the test. Calcineurin is a key regulator of signal transduction. The interaction between Spt20 and Ppb1 was confirmed by yeast two-hybrid assay and co-immunoprecipitation. In S. pombe, ppb1delta was hypersensitive to high concentration of Cl-. In contrast, spt20delta could resist high concentration of Cl-, which maintained normal growth of cells. Fluorescent colocalization analysis showed that Ppb1 was translocated from cytoplasm to nucleus and colocalized with Spt20 upon the increase of extracellular Cl-. Further genetic analysis revealed that loss of spt20+ suppressed the hypersensitive phenotype to Cl- of ppbldelta. Thus, spt20+ and ppb1+ stayed in the same pathway of regulating Cl- homeostasis and spt20+ functioned downstream of ppb1+. Our data suggest that spt20delta is able to resist high concentration of extracellular Cl- and Spt20 involves in the calcineurin-mediated Cl- homeostasis. The aberrant up-regulation of intracellular Cl- is correlated with the diseases like myocardial ischemia reperfusion injury in higher organism. As Spt20 is highly conserved in eukaryotes, it might serve as a potential drug target in Cl- imbalance related diseases.