A linear stability analysis is performed in this paper to explore the instability characteristics of nanofluids in a horizontal porous medium uniformly heated from below. The theory employs Buongiorno’s model for nanofluids and Brinkman model for porous media, and the results are restricted to the case with high porosity in order to avoid the particles interacting with the walls of the pores. Different from the previous studies, a novel base-state solution is derived by considering the dependence of thermophoresis on particle concentration. The solution of concentration turns out to be a nonlinear function in terms of NA (a parameter denoting the relative strength of thermophoresis and Brownian diffusion for nanoparticles). As NA is large, the thermophoretic effect prevails over Brownian diffusion and drives the particles into the upper region of layer, which substantially changes the stability. Results show that the system is extremely unstable for common nanofluids as long as the layer is heated from below. Since the neutral curve does not exist, the dispersion spectra are created instead to illustrate the instability characteristics. It is found that the thermophoretic effect together with buoyancy is a very strong destabilizing mechanism that is sufficient to overcome the Darcy resistance and trigger the onset of convection in porous media.