In this paper, a new Doppler technique based on pulse subtraction imaging (PSD) is described and compared with pulse inversion Doppler (PID). Combining a nonlinear contrast agent imaging technique with a Doppler process provides a tool for detecting motion of both contrast agents and tissues. This has potential in targeted imaging in which attached microbubbles need to be separated from moving ones and surrounding tissues. The results from both simulation and experiment show that PSD is able to differentiate bubble motion from tissue motion. For Doppler processing conducted at the fundamental frequency, the contrast-to-tissue ratio (CTR) in PSD was 3.3 (±0.4) times higher on average than PID at a mechanical index (MI) of 0.1. At the harmonic frequency, PID was shown to have a 3.1 (±0.4) times higher CTR than PSD. Overall, taken in their optimum processing conditions, PID has a CTR up to 1.9 (±0.4) times higher than PSD. The CTRs for both techniques have also been shown to increase with increasing MI. However, for the same axial Doppler resolution. PSD also allows less energy to be transmitted into the medium, which makes it less disruptive. The relative performances of PSD and PID in terms of the bandwidth of the imaging system are also discussed.