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We present a method to determine junction temperature in GaN-based laser diodes (LDs) for simple, fast, and reliable characterization of thermal properties. The large change of forward operation voltage with temperature in GaN laser diodes is advantageously used to measure junction temperature. Using this method, we compare junction temperature of LD structures with different substrates and chip mounting methods. It is found that the junction temperature can be reduced considerably by employing GaN substrates or epi-down bonding. For epi-down bonded LDs, as much as two-fold reduction in junction temperature is achieved compared to epi-up bonded ones and junction temperature rise in this case is only about 13 degrees for more than 100 mW-output power.