This paper describes and analyzes a various generation methods of the mutually orthogonal polyphase sequences with low cross-correlation peak sidelobe and low autocorrelation peak sidelobe levels. The mutual orthogonality is the key requirement of multi-static or MIMO(Multi-Input Multi-Output) radar systems which provides the good target detection and tracking performance. The polyphase sequences, which are generated by SA(Simulated Annealing) and GA(Genetic Algorithm), have been analyzed with ACF(Autocorrelation Function) PSL(Peak Sidelobe Level) and CCF(Crosscorrelation Function) level at the matched filter output. Also, the ambiguity function has been introduced and simulated for comparing Doppler properties of each sequence. We have suggested the phase selection rule for applying multi-static or MIMO systems.