Apparatus for controlling an automotive air conditioner comprises first and second air distribution passageways in which blower fans are provided to direct air streams respectively therethrough to first and second areas of a passenger compartment. First and second evaporators located in the first and second passageways respectively are supplied with working fluid to transfer thermal energy from the first and second air streams to the supplied working fluid. A control unit is responsive to the temperatures of the first and second areas and temperature settings for estimating thermal energies of the first and second air streams to be delivered from the passageways and derives first and second control signals from the estimated thermal energies to control actuators which individually regulate the flow rates of the working fluid supplied to the first and second evaporators.