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Located below the air filter box on top of the transmission in the 2006 Hyundai Sonata. To change the transmission fluid, start by ensuring that the car is parked on level ground and then opening the hood. Locate the transmission fluid reservoir, which should be situated on or near the transmission itself, and locate the dipstick. Remove it, clean it, reinsert it, and then pull it out again. Take note of the fluid level indicated and determine how much additional fluid is needed to fill the reservoir. Use a funnel to add fluid until it reaches the full mark, or slightly below. Avoid overfilling. Close the reservoir and you're good to go.
In the 2006 Hyundai Sonata, you can locate the transmission control module inside the transmission towards the back of the case, under the end cover.