Audio Frequency Shift Keying to Arduino
Can you give any more detail on the frequency of the signal. A 60 and 100 Hz signal is a different ball game than 60 and 61 Hz which is significantly harder to diagnose and is completely different from 6 and 7 GHz.

For 60 and 100Hz of dependable amplitude I would just use a schmitt trigger and count the time between rising edges.
-Max Murphy