Compared with other vertebrate animal models, zebrafish (Danio rerio) has its superior advantages for studying stem cell migration. Zebrafish have similar tissues and organs as mammals, where tissue-specific stem cells reside in. Zebrafish eggs are externally fertilized and remain transparent until most of the organs are fully developed. This allows imaging stem cells in vivo very easily. Recently, a zebrafish double pigmentation mutant, casper, became a new popular imaging model in the zebrafish field due to its completely transparent bodies in adulthood. It has been used as an excellent model to study adult hematopoietic stem cell (HSC) in the transplantation setting. The unparalleled imaging power of zebrafish provides great opportunities of tracing stem cells in vivo in the developmental and regenerative context. In this chapter, we use HSC as an example and combine the powerful imaging techniques in zebrafish, to provide protocols for in vivo imaging fluorescence-labeled stem cell migration, stem cell fate tracing in zebrafish embryos, HSC transplantation, and in vivo imaging in both zebrafish embryos and adults. These techniques can also be applied to other types of stem cells in zebrafish embryos and adults.