In this paper, we propose a method --based on the discrete evolutionary transform (DET)-- to estimate the instantaneous frequency of a signal embedded in noise or noise-like signals. The DET provides a representation for non-stationary signals and a time-frequency kernel that permit us to obtain the time-dependent spectrum of the signal. We will show the instantaneous phase and the corresponding instantaneous frequency (IF) can also be computed from the evolutionary kernel. Estimation of instantaneous frequency is of general interest in time-frequency analysis, and of special interest in the excision of jammers in direct sequence spread spectrum. Implementation of the IF estimation is done by masking and a recursive non-linear correction procedure. The proposed estimation is valid for monocomponent as well as multicomponent signals in the noiseless and noisy situations. Its application to jammer excision in direct sequence spread spectrum communication is considered as an important application. The estimation procedure is illustrated with several examples.