The objective of this paper is to clarify the role of thermophoresis in laminar natural convection in a Rayleigh–Benard cell filled with a water-based nanofluid and to study its relative importance compared to other effects, in an attempt to correct the present confusing interpretation of the magnitude of the thermophoresis coefficient in nanofluids. The major forces are introduced and the transport equations are solved using a two-phase lattice Boltzmann method (LBM) for a laminar flow with Ra numbers up to 106 with various particle loadings (particle volume fractions). The results indicate an increase in the average Nu number with an increase in the Ra number and particle loading. An increase in the Nu number for a 10% particle loading at Ra = 106 is less than 20%. When thermophoresis effect is taken into consideration, an increase in the Nu number is predicted, which is about 10%. Therefore, it is concluded that using a nanofluid in bottom-heated laminar natural convection results in a considerable increase in heat transfer rate and thermophoresis force is a significant contributor to heat transfer augmentation, particularly for high Ra numbers (Ra ∼ 106 and higher). It is observed that at low Ra numbers (weak convective flows), the nanofluid behaves homogenously, but at higher Ra numbers, it starts to behave heterogeneously.