Melanoidin containing wastewater is generated from the distillation process in bioethanol production system. In this study, the melanoidin in water was decomposed by ozone microbubbles and the effect of operation conditions on the decolorization and the total organic carbon (TOC) was investigated. A rectangular tank was made from transparent acrylic resin. A microbubble generator utilizing liquid shear stress, consisting of a liquid pump and a special line mixer, was set at the side of the tank. For comparison, a sintered glass gas sparger was used to generate millimeter sized bubbles. A melanoidin aqueous solution was prepared from glycine and glucose using an autoclave. Compared with ozone millibubbles, the melanoidin in water was effectively decomposed by ozone microbubbles. The volumetric mass transfer coefficient of ozone for microbubbles was much higher than that for millibubbles. The decomposition of melanoidin in water was enhanced by incrementing ozone concentration and flow rate of sparging gas. In the case of decolorization, the reaction rate obeyed a pseudo-first order reaction and the apparent rate constant became higher at pH = 4.0 with a radical trap agent. The decolorization of melanoidin was mainly attributed to direct ozone oxidation. The apparent decolorization rate constant increased with decreasing temperature and the rate-controlling step of decolorization was the ozone dissolution into water. On the other hand, the TOC reduction rate increased by the hydroxide radical generated by ozone self-decomposition. The TOC reduction rate increased with increasing temperature. The combination of ozone microbubbles and biological treatment was effective in the treatment of melanoidin containing wastewater.