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The interaction between homochiral substituted perylene bisimide (PBI) molecule and the D enantiomer of phenylalanine amino acid was monitored. Spectroscopic transitions of PBI derivative in aqueous solution in the visible range were used to evaluate the presence of D-phenylalanine. UV-visible, fluorescence, FT-IR, and AFM characterizations showed that D-phenylalanine induces significant variations in the chiral perylene derivative aggregation state and the mechanism is enantioselective as a consequence of the 3D analyte structure. The interaction mechanism was further investigated in presence of interfering amino acid (D-serine and D-histidine) confirming that both chemical structure and its 3D structure play a crucial role for the amino acid discrimination. A D-phenylalanine fluorescence sensor based on perylene was proposed. A limit of detection (LOD) of 64.2 ± 0.38 nM was calculated in the range 10–7–10–5 M and of 1.53 ± 0.89 μM was obtained in the range 10–5 and 10–3 M.