Ions of the title compound, C(6)H(15)N(2)O(2) (+)·C(2)F(3)O(2) (-), a new organic nonlinear optical crystal, are linked by N-H⋯O hydrogen-bonding inter-actions. Both the amino groups of the l-lysinium cation are protonated. A three-dimensional network of hydrogen bonds is observed, forming a closed ring. Inter-molecular N-H⋯O hydrogen bonds involving l-lysinium cations and trifluoro-acetate anions link the ions into extended chains which run parallel to the [010] direction. The F atoms of the trifluoro-acetate anion are disordered over two sites with site occupancies of 0.423 (18) and 0.577 (18). The asymmetric unit consists of two cations and two anions.