A weakly fluorescent cobalt(II) complex is synthesized using 2-(2-pyridyl)-benzimidazole (PBI) as a chelating fluorescent ligand and characterized by single crystal X-ray structure. This complex serves as an efficient fluorescent probe for trace level determination of aspartic acid (AspA) and glutamic acid (GluA) in aqueous solution. Rest of the naturally occurring amino acids did not interfere. Both aspartic acid and glutamic acid replaces PBI from the coordination sphere of Co(II)-PBI complex resulting appearance of strong fluorescence signal for the released free PBI. The signal response is very fast and the interaction of both the AspA and GluA with the Co(II) is strong enough as evident from their displacement equilibrium constant values, viz. 4357.8 M−1 and 8333.33 M−1 respectively.