The stabilization energies for the formation (E(form)) of 11 ion pairs of protic and aprotic ionic liquids were studied by MP2/6-311G** level ab initio calculations to elucidate the difference between the interactions of ions in protic ionic liquids and those in aprotic ionic liquids. The interactions in the ion pairs of protic ionic liquids (diethylmethylammonium [dema] and dimethylpropylammonium [dmpa] based ionic liquids) are stronger than those of aprotic ionic liquids (ethyltrimethylammonium [etma] based ionic liquids). The E(form) for the [dema][CF3SO3] and [dmpa][CF3SO3] complexes (-95.6 and -96.4 kcal/mol, respectively) are significantly larger (more negative) than that for the [etma][CF3SO3] complex (-81.0 kcal/mol). The same trend was observed for the calculations of ion pairs of the three cations with the Cl(-), BF4(-), TFSA(-) anions. The anion has contact with the N-H bond of the dema(+) or dmpa(+) cations in the most stable geometries of the dema(+) and dmpa(+) complexes. The optimized geometries, in which the anions locate on the counter side of the cations, are 11.0-18.0 kcal/mol less stable, which shows that the interactions in the ions pairs of protic ionic liquids have strong directionality. The E(form) for the less stable geometries for the dema(+) and dmpa(+) complexes are close to those for the most stable etma(+) complexes. The electrostatic interaction, which is the major source of the attraction in the ion pairs, is responsible for the directionality of the interactions and determining the magnitude of the interaction energy. Molecular dynamic simulations of the [dema][TFSA] and [dmpa][TFSA] ionic liquids show that the N-H bonds of the cations have contact with the negatively charged (oxygen and nitrogen) atoms of TFSA(-) anion, while the strong directionality of the interactions was not suggested from the simulation of the [etma][CF3SO3] ionic liquid.