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Background: Recently, the pulse-in-pulse mode of intense pulsed light (IPL) has been used increasingly for the treatment of melasma. Objective: To observe the morphologic changes in the melanophore in adult zebrafish after irradiation with conventional and pulse-in-pulse IPL and Q-switched Nd:YAG (QSNY) laser. Methods: Adult zebrafish were irradiated with conventional and pulse-in-pulse mode of IPL. The conditions for conventional IPL were 3 mJ/cm2, 560 nm filter, and pulse widths of 7, 20, and 35 msec. The pulse-in-pulse conditions were 3 mJ/cm2 and on-time 1/off-time 2. The QSNY laser was used with the settings of 1,064 nm, 0.4 J/cm2, a 7 mm spot size, and one shot. Specimens were observed using a light microscope, a transmission electron microscope (TEM), a scanning electron microscope (SEM) and a confocal microscope. Results: After conventional IPL irradiation with a 7 msec pulse width, melanophore breakage was observed using light microscopy. Under TEM, irradiation with conventional IPL for 7 msec and pulse-in-pulse IPL induced melanophore thermolysis with vacuolization. However, changes in the melanophore were not observed with 35 msec IPL. Under SEM, unlike the control and QSNY groups, IPL-irradiated zebrafish showed finger-like fusion in the protein structure of scales. Specimens examined by a confocal microscope after conventional IPL irradiation showed a larger green-stained area on TUNEL staining than that after pulse-in-pulse mode IPL irradiation. Conclusion: Zebrafish irradiated with long pulse-IPL showed no morphologic changes using light microscopy, while morphological changes in melanophores were evident with use of TEM. Pulse-in-pulse mode IPL caused less damage than conventional IPL.