Objective To investigate hair follicle morphogenesis of different hoof periphery site, SHH and β-catenin temprocal-spatial expression during hair follicle morphogenesis. Methods Totally 41 embryonic 45-248 days Yak embryos forepaw were used as material to investigate hair follicle morphogenesis of different hoof periphery site by HE staining and immunohistochemistry of tissue section for detecting temprocal-spatial expression and epithelial-mesenchymal reciprocal interaction during morphogenesis. SHH expression during hair follicle morphogenesis showed stronger effect on the hair follicle epidermis than the hair follicle mesenchyme. Results The hair follicle morphogenesis of yak proximal hoof end and distal hoof end initiate from embryonic 45 days and initiate from embryonic 55 days respectively, mature hair follicle in embryonic 120 days. From the proximal hoof end to distal hoof end, the time,the phase,the size and the growing depth of the hair follicle morphogenesis in turn showed a occure degressive gradient. β-catenin expression during hair follicle morphogenesis showed a stronger effect on the hair follicle epidermis than the hair follicle mesenchyme.Conclusion We speculate that SHH and β-catenin expression and detail function difference play important roles during hair follicle morphogenesis in different hoof periphery site of yak embryos. The epidermis is dominated during the hair follicle mor