In vivo micromanipulation using ultrasound is an exciting technology with promises for cancer research, brain research, vasculature biology, diseases, and treatment development. In the present work, we demonstrate in vivo manipulation of gas-filled microparticles using zebrafish embryos as a vertebrate model system. Micromanipulation methods often are conducted in vitro, and they do not fully reflect the complex environment associated in vivo. Four piezoelectric actuators were positioned orthogonally to each other around an off-centered fluidic channel that allowed for two-dimensional manipulation of intravenously injected microbubbles. Selective manipulation of microbubbles inside a blood vessel with micrometer precision was achieved without interfering with circulating blood cells. Last, we studied the viability of zebrafish embryos subjected to the acoustic field. This successful high-precision, in vivo acoustic manipulation of intravenously injected microbubbles offers potentially promising therapeutic options.