That's very simple: You tell it the FFT, by defining in what time window you take the samples! When doing a FFT you cut out a certain time period of a function in the time domain, in your case the period of time between two succeeding zero crossings, and assume that this period is repetitively continued for an infinte number of times. The FFT then tells you by what sine and cosine functions (fundamental and harmonics) you could fabricate this signal. And the fundamental automatically has a period which by theory of FFT exactly equals the duration of time period within you take the samples!

Kai