A control apparatus for an engine has a crankshaft position sensor that generates an output signal indicating the rotational position of a crankshaft. The output signal has at least one discontinuous portion per rotation of the crankshaft indicating a reference position of the crankshaft. The timing of an engine operating parameter such as the timing of fuel injection or ignition is calculated and controlled so as to occur with the calculated timing using the reference position as a reference. A camshaft position sensor senses the rotation of a camshaft and generates a signal having pulses occurring between consecutive occurrences of the reference position. The cylinders of the engine are identified by counting the number of pulses occurring between the reference positions.