We have developed a method for simultaneous source separation using time dithering and encoded source sequences. The source sequences are designed so that they are close to orthogonal to each other, having minimized crosscorrelation and optimal autocorrelation properties. We found that this additional encoding of time-dithered sources could be exploited with a multifrequency separation method. The separation method relies on a coherency-based approach and is solved by a sparse Radon inversion. Realistic synthetic data examples confirmed the importance of using the multifrequency method to take advantage of the sequence orthogonality and to deal with spatially aliased data. Our results demonstrate that source sequence encoding can significantly improve simultaneous source separation compared with using time dithering only.