Fluorescent labeling of DNA was studied by using two newly synthesized ligands, which are 4-(2-hydroxybenzylidinamino) benzoic acid (PHBA) and 4-(2-hydroxybenzylidinamino) phthalic acid (PHPA). Their binding capacity to calf-thymus DNA was determined on functionalized superparamagnetic iron oxide nanoparticles (SPIONs). 23.1 µg of DNA was immobilized on 25 mg of nanoparticles. Binding capacity of fluorescent ligands to DNA-APTS-SPIONs was also found as 2.36 µM for PHBA and 1.97 for PHPA at 25 mg of the nanoparticles. Binding of the DNA to the ligands were examined by scanning electron microscopy, transmission electron microscopy, infrared spectroscopy, and confocal microscopy.