This research purposes to identify the fungi level on some fermentation box type and duration (three and five days). Gunungkidul and Kulonprogo is the highest cocoa producing areas in Yogyakarta. Each region has different habits in using fermentation box. The fermentation box types are the basket (the fermentation box that being use commonly in Gunungkidul, storey box (Kulonprogo) and single box with a hand crank (introduction fermentation box). This is important, because each fermentation box type drive a quality range of cocoa beans. These results are expected to identify which boxes and duration providing the lowest fungi level contaminant. Whereas, the benefit of this study is produces an efficient box design for better fermentation process with fungi levels low.