Temperate mycobacteriophage L1 encodes an unusual repressor (CI) for regulating its lytic-lysogenic switching and, in contrast to the repressors of most temperate phages, it binds to multiple asymmetric operator DNAs. Here, ions like $Na^+$, $Cl^-$, and $acetate^-$ ions were demonstrated to facilitate the optimal binding of CI to cognate operator DNA, whereas $K^+$, $Li^+$, ${NH_4}^+$, $Mg^{2+}$, $carbonate^{2-}$, and $citrate^{3-}$ ions significantly affected its operator binding activity. Of these ions, $Mg^{2+}$ unfolded CI most severely at room temperature and, compared to $Mg^{2+}$, $Na^+$ provided improved thermal stability to CI. Furthermore, the intrinsic tryptophan fluorescence of CI was changed notably upon replacing $Na^+$ with $Mg^{2+}$ and these opposing effects of $Mg^{2+}$ and $Na^+$ were also noticed in their actions on the C-terminal fragment (CTD) of CI. Taken together, $Na^+$ appeared to be more appropriate than $Mg^{2+}$ for maintaining the biologically active conformation of CI needed for its optimal binding to operator DNA.