A new algorithm of color Doppler mapping of one specific velocity of biological liquids with shuttle flows using optical coherence tomography is presented. The algorithm does not have the disadvantage 2π-ambiguity of color Doppler images. It is realized using the separation of the raw data to two parts corresponding to positive and negative shifts of the carrier frequency. As a final result, the complexation of independently reconstructed structural image and 2D color-coded one specific velocity image is performed. The practical implementation of the algorithm was performed in the LabVIEW package using the stream programming. A blood vessel hydrodynamic phantom was used for testing and debugging the final software product.