The present invention relates to an air conditioner for a vehicle including a front seat air conditioning unit and a rear seat air conditioning unit. The rear seat air conditioning unit has a rear seat air conditioning casing provided with a rear seat evaporator disposed substantially in the horizontal direction to air flow passages therein, with a rear seat heater core disposed on the upper side of the rear seat evaporator, with rear seat vent outlets and rear seat floor outlets disposed on the upper and lower portions of the exit end thereof for discharging the air flowing to the rear seats of the vehicle, with a bypass flow passage formed along the outer side of the rear seat heater core, with an air mixing area portion where the air passed through the rear seat evaporator is mixed with the air passed through the rear seat heater core, with a rear seat partition wall for dividing the air flow passages into two areas, with first rear seat temperature doors disposed between the rear seat evaporator and the rear seat heater core, and second rear seat temperature doors for opening and closing the lower air flow passage of the rear seat heater core.