The aim of this study is to explore the active components of Anoectochilus roxburghii capable of inhibiting melanin formation using chemical separation and extraction and functional analysis. Anoectochilus roxburghii were extracted with alcohol and separated into three groups: the total extraction group, alcohol extracted group and alcohol precipitated group. Zebrafish embryos at 0.75 h post-fertilization were exposed to various concentrations of the three groups of extracts, and analyzed at 72 h, using semi-quantitative RT-PCR and in situ hybridization. The results showed that the alcohol extracts inhibit melanogenesis most significantly in the zebrafish embryos. The mRNAs of melanin-related genes, such as silv, tyr, tyrp1a, were down-regulated by the alcohol extracts spatially and temporally. The alcohol extracts also inhibited the activity of tyrosinase, a key enzyme in melanogenesis, in a dosage dependent manner. In addition, the alcohol extracts also display a remarkable inhibitory effect on melanin synthesis through down-regulation of mRNAs of melanin-related genes and tyrosinase activity in zebrafish embryos, in which a large amount of melanin has already been synthesized. Such inhibitory effect could be reversed after the withdrawal of the alcohol extracts. Our results showed that the alcohol extracts of Anoectochilus roxburghii can significantly inhibit zebrafish melanogenesis, supporting the notion that Anoectochilus roxburghii could potentially be used in the development and production of natural whitening products.