The ability of heartwood extract ofMorus bombycis in controlling the melanogenesis in B16 melanoma was investigated. An inhibitory effect was observed when the dose concentration was less than 10 mg/L. When the dose was 10 mg/L, the extracellular melanin accumulated was only 5% of the control. Proteome analysis with 2-D PAGE and MALDI-TOF showed that there were various proteins involved in inhibitory melanogenesis. It seems that down-regulation of TRP2, vacuolar protontranslocating ATPase 100 kDa subunit isoform a1-I and V-ATPase E2 subunit were involved in melanosome development and regulation that could reduce melanin synthesis.