The in-plane thermal conductivity of silicon phononic membranes is investigated by micro time domain ther-moreflectance and Monte Carlo simulations. Strong reduction of thermal conductivity is observed mainly due to phonon boundary scattering for both aligned and staggered lattices of holes. The measured and calculated thermal conductivities of the porous membranes with cylindrical holes are found to be in good quantitative agreement (at 4 K and 300 K). A significant difference between thermal conductivities of aligned and staggered lattice of identical porosities is observed. This difference is shown to arise from ballistic phonons that acquired directionality by propagating between the holes. The directionality effect strengthens when the temperature is decreased or when the diameter of the holes becomes close to the period. Finally, we propose a model, which quantifies and explains the difference between thermal conductivities of aligned and staggered lattices based on geometric considerations.