Fluorescence imaging technology using two-photon excitation microscopy has been developed and utilized to observe cell dynamics in various developmental processes and pathological conditions in vivo. This technology is absolutely dependent on the fluorescent labelling technique of specific cells in a living state in vivo using various methods such as genetic engineering, chemiluminescent probes or fluorescent-conjugated antibodies. In this article, we demonstrate the methods of genetic engineering, particularly how to generate a genetically modified mouse(reporter mouse)that expresses fluorescent protein endogenously in the specific cells. In consideration of mouse genetic engineering technologies and the current state of bioresources, we describe the transgenic method, the knock-in method, the Cre/loxP-mediated recombination method and the genomic editing method by CRISPR/Cas9 system that have been used widely for generation of reporter mice. Among these methods, it is important to carefully select the suitable method according to the research purpose. We would like to compare the methods comprehensively.