The heat shock promoter is useful for regulating transgene expression in small water-living organisms. In zebrafish embryos, downstream gene expression can be greatly induced throughout the body by raising the temperature from 28.5°C to 38.0°C. By manipulating the local temperature within an embryo, spatial control of transgene expression is also possible. One such way for inducing heat shock response in targeted cells is by using a laser microbeam under the microscope. In addition, random mosaic expression by transient gene expression and transplantation of the transgenic embryo into a wild type host can be considered a powerful tool for studying gene functions using this promoter. In this paper, we review the applications of the zebrafish heat shock protein promoter as a gene expression tool and for lineage labeling and transcription enhancer screening.