We aimed to identify major differentially expressed genes of embryonic fibroblasts from chicken embryos. We examined the layer, Beijing Fatty Chicken (BFC), and broiler, Silkie Bantam (SB), two distinctive chicken breeds. Nine-day old chicken embryos are developmentally between the beginning of feather formation and the beginning of hardening of the beak. Embryonic fibroblasts are most abundant at this stage. In this paper we used microarray to compare transcriptional levels, and found the different expression of some genes related to signaling pathways involved in fibroblast development. Subsequent real time-PCR was consistent with microarray data. Therefore, the results described herein provide insightful information for animal husbandry and scientific research.