Melanoblasts originating from neural crest cells can migrate through the mesenchyme of the developed embryo and give rise to melanocytes. Unlike the melanocytes that are confined to the integument in other vertebrates, melanocytes in Silky Fowl can reach the ventral regions of the embryos owing to differences in gene expression in the process of melanoblasts migration. In this study, we used microarray profiling to identify differences in gene expression between White Leghorn and Silky Fowl. Differential expression of 2517 microarray probes ( <0.01, Fold Change>2) was observed in Silky Fowl compared to White Leghorn. After filtration by cluster analysis, functional annotation and pathway analysis, eight differentially expressed genes were identified to be closely related to the development of melanocytes. Moreover, differences in expression of immune genes were also detected between Silky Fowl and White Leghorn. The differentially expressed genes associated with melanocyte development were verified by q-PCR, and results were highly consistent with the microarray data. The genes with significantly altered expression involved in melanoblast migration and development suggested that different microenvironments resulted in the abnormal melanoblast migration in Silky Fowl, although there were no big differences in melanoblast development between these two breeds. The candidate genes discovered in this study are beneficial to understand the molecular mechanism of hyperpigmentation in Silky Fowl.