This paper describes a low-cost and flexible vegetation monitoring system and compares it with traditional remote sensing systems such as airplanes and satellites. We have developed a small unmanned aerial vehicle (UAV) equipped with visible and infrared cameras for vegetation observation. This system can automatically generate widespread high-resolution mosaic image and calculate the vegetation index from the multiple aerial images collected by an autonomous flight of the UAV. We performed monitoring experiments at Yawata moor in Hiroshima Prefecture. From the experimental results, we concluded that the small UAV system was effective and useful for carrying out low-cost and flexible vegetation monitoring.