High genetic differentiation in natural populations of Pinus henryi and Pinus tabuliformis as revealed by nuclear microsatellites

► We surveyed population genetic structure among populations of P. henryi and P. tabuliformis using nuSSRs. ► High genetic differentiation was found. ► The dividing line of the two pines lay between Qing-Daba Mountains. ► Interspecific divergence was caused by habitat differences. ► Recent unilateral migration was due to expansion driven by global warming.