We established three lines of transgenic medaka, a heat-shock element (HSE) monitor line (hse-GFP line), heat-inducible driver lines (hse-cre lines), and effector lines (gapdh-loxP[DsRed]-GFP lines). We employed these to comprehensively analyze gene induction at different time points in various tissues. These analyses demonstrate a good response of synthetic HSEs by heat treatment during embryogenesis and the mosaic gene induction by cre/loxP-mediated recombination, thus providing practical information regarding the feasibility of a heat-inducible cre/loxP-mediated system in medaka. We also activated recombination by local heat-treatment using a metal probe and an infrared laser. Our results collectively indicate that these lines allow us to perform lineage tracing and mosaic analysis and provide the platform to investigate gene functions at later developmental stage and adult. genesis 51:59–67, 2013. © 2012 Wiley Periodicals, Inc.