The capacitance-voltage (C-V) measurements of GaN-based Schottky diodes were carried out in the frequency range of 0.3～1.5MHz. Anomalous peaks and negative value of capacitance were observed in the C-V plots of Au/i-GaN Schottky diodes under forward bias, while neither of them was seen in the plots of Au/i-Al0.45Ga0.55N Schottky diodes. Based on the parameters extracted from the current-voltage (I-V) and C-V plots of GaN and Al0.45Ga0.55N Schottky diodes, the peak and negative capacitance are ascribed to the capture and loss of interface charges. These processes are greatly suppressed when there exists a huge series resistance in the diode.