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I am using an Arduino UNO R3 to generate a PWM signal, the user sets the duty cycle using the serial monitor. The Arduino output signal is correct, but when the signal is connected to the input of the gate driver IC (IR2104) the low side driver output shows the signal with the compliment of the duty cycle (1-D)? why? I am using this IC to drive an IRFZ44N MOSFET.

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The datasheet shows on page 4, under "lead defintions":

IN: Logic input for high and low side gate driver outputs (HO and LO), in phase with HO

In addition, the functional block diagram shows the input for the low side driver being inverted. Excerpt from IR2104 datasheet

Thus, when IN is high, the top side MOSFET is on and the bottom one is off.

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when the signal is connected to the input of the gate driver IC (IR2104) the low side driver output shows the signal with the compliment of the duty cycle (1-D)? why?

That's what this chip produces: -

enter image description here

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