We propose a label-free system that estimated the concentration of DNA droplets in sub-microliter volume based on the impedance measurement method. A USB oscilloscope with a built-in function generator was employed to reduce the system size instead of existing lock-in amplifiers or network analyzers. An electrode pair was fabricated with patterns on a printed circuit board (PCB). To minimize the measurement variation of the impedance between experiments, the electrode was made hydrophilic and the periphery of the electrode was blocked with a hydrophobic substance to prevent the droplet from spreading. For this purpose, the hydrophilicities of gold, tin, and silver coatings available in the PCB fabrication process and the hydrophobicities of various materials were investigated to select the most hydrophilic material to be used for the electrode coating. The proposed system was evaluated with various concentrations of saline solution and Chlamydia trachomatis DNA. Multiple measurements for a day experiment were performed for several days to investigate the precision of the proposed system. The measurement coefficient of variation (CV) of the proposed system was less than 3.7% for saline solution and 1.8% for DNA solution, showing that the proposed system is sufficiently precise.