This chapter provides insight into the microfluidic domain that involves magnetic particles, in particular, the transport of ferrofluids and magnetic microspheres. It discusses “Magnetic Microspheres” that the particle–particle dipolar interactions are important for a dense suspension under the influence of a magnetic field. The most common magnetic particles used for microfluidic applications are single domain iron oxide nanoparticles of 5–15 nm diameter. The proper choice of ferrofluids and the suitable surface modification of microchannel walls are essential for successful implementation of ferrofluid plungers in a microfluidic device. In droplet-based microfluidic applications, samples and reagents are enclosed in microdroplets on flat substrates or in immiscible fluids. The transport of magnetic microspheres in a microfluidic channel occurs in a strongly viscosity-dominated regime because the particle Reynolds number is extremely low for these particles. The on-chip manipulation of droplets consisting of a suspension of magnetic microspheres can merge, mix, and separate droplets on a microfluidic platform.