Following the emergence of many novel two-dimensional (2-D) materials beyond graphene, interest has grown in exploring implications for fundamental physics and practical applications, ranging from electronics, photonics, phononics, to thermal management and energy storage. In this Colloquium, we first summarize and compare the phonon properties, such as phonon dispersion and relaxation time, of pristine 2-D materials with single layer graphene to understand the role of crystal structure and dimension on thermal conductivity. We then compare the phonon properties, contrasting idealized 2-D crystals, realistic 2-D crystals, and 3-D crystals, and synthesizing this to develop a physical picture of how the sample size of 2-D materials affects their thermal conductivity. The effects of geometry, such as number of layers, and nanoribbon width, together with the presence of defects, mechanical strain, and substrate interactions, on the thermal properties of 2-D materials are discussed. Intercalation affects both the group velocities and phonon relaxation times of layered crystals and thus tunes the thermal conductivity along 2 both the through-plane and basal-plane directions. We conclude with a discussion of the challenges in theoretical and experimental studies of thermal transport in 2-D materials. The rich and special phonon physics in 2-D materials make them promising candidates for exploring novel phenomena such as topological phonon effects and applications such as phononic quantum devices.