Monte Carlo simulation is applied to investigate phonon transport in single crystalline Si nanowires. Phonon-phonon normal (N) and Umklapp (U) scattering processes are modeled with a genetic algorithm to satisfy energy and momentum conservation. The scattering rates of N and U scattering processes are found from first-order perturbation theory. The thermal conductivity of Si nanowires is simulated and good agreement is achieved with recent experimental data. In order to study the confinement effects on phonon transport in nanowires, two different phonon dispersions, one from experimental measurements on bulk Si and the other solved from elastic wave theory, are adopted in the simulation. The discrepancy between simulations using different phonon dispersions increases as the nanowire diameter decreases, which suggests that the confinement effect is significant when the nanowire diameter approaches tens of nanometers. It is found that the U scattering probability in Si nanowires is higher than that in bulk Si due to the decrease of the frequency gap between different modes and the reduced phonon group velocity. Simulation results suggest that the dispersion relation for nanowires obtained from elasticity theory should be used to evaluate nanowire thermal conductivity as the nanowire diameter is reduced to the sub-100 nm scale.