In this study, a sensor system was designed to detect metal ions based on the fluorescence resonance energy transfer (FRET) process between free-phthalocyanine (PC) and merocyanine 540 (MC540). Following the determination of parameters and appropriate conditions for energy transfer, the sensor system was tested with different metal ions. The conclusion was that the system showed high selectivity to iron and aluminum ions. In this FRET system, limit of detection (LOD) values for metal ions were calculated as 437 nM for Al(3+)and 32.1 nM for Fe3+. The system was able to detect iron and aluminum in very low concentrations. It also showed good selectivity for the two metal ions.