High frequency fluctuation in the optical signal generated in Fourier-Domain Mode Locked fiber laser (FDML-FL), which is the major problem and degrades the laser performance, is not yet fully analyzed or studied. The basic theory which is causing this high frequency fluctuation is required to clearly understand its dynamics and to control it for various applications. In this letter, by analyzing the signal and system dynamics of FDML-FL, we theoretically demonstrate that the high frequency fluctuation is induced by the intrinsic instability of frequency offset of the signal in cavity with nonlinear gain and spectral filter. Unlike the instabilities observed in other laser cavities this instability is very unique to FDML-FL as the central frequency of the optical signal continuously shifts away from the center frequency of the filter due to the effects like dispersion and/or nonlinearity. This instability is none other than the Eckhaus instability reported and well studied in fluid dynamics governed by real Ginzburg-Landau equation.
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