Phase Difference between two Signals ?

I've to calculate phase difference between two sampled signals having the same frequency at any instant but not fixed frequency (40KHz - 50KHz).

1. Which algorithm should I use to calculate the phase difference between two signals to obtain accurate result ? FFT , Correlation or any other ?

2. Does the accuracy of calculated phase difference depends on the sampling frequency ?

I'm new to digital signal processing So, correct me if I'm wrong.

[Walter Roberson]

Are the two signals each frequency modified (FM) sine waves?

[rahul]

These two signals are VOLTAGE AND CURRENT (sine waves) feedback signals from ultrasonic transducer.

For resonating (to drive at minimum impedance..Purely resistive) the transducer we have to maintain zero degree phase relation between V & I signals. That can be achieved by changing signals frequency proportionally and check whether the phase difference of zero has been achieved at that new frequency.

So in time domain signal can be viewed to be as discrete FM... where phase & frequency abruptly changes, phase starting from 0 and frequency which might be few 10Hz away from the last driven frequency.