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Some imidazolium-based ionic liquids were used to determine zwitterionic or non-zwitterionic structures of glycine and p-amino benzoic acid, as model amphoteric compounds, in their corresponding isoelectric point. To do this, the partitioning behaviors of both compounds between the ionic liquid and aqueous phase at different pH values were investigated. The results revealed that due to having different pH-dependent chemical structures, each compound showed different partitioning behavior. This observation was considered as a basis for introducing a green technique for understanding the real chemical structures (species), i.e. zwitterionic or non-zwitterionic structures of amphoteric compounds such as amino acids in the aqueous solutions. This study revealed the existence of a non-zwitterionic (neutral) structure for p-amino benzoic acid and a zwitterionic structure for glycine in their corresponding isoelectric points.