To analyze the evolutionary level of Prunus mira Koehne (Prunus mira Koehne Kov et. Kpst), 15 kinds of pollen grains from five altitudes were observed using a scanning electron microscope (SEM). This study demonstrates that pollen morphous P. mira has high variation; specifically, individuals from higher altitudes are much more evolved than those from lower altitudes. This is the first time the pollen morphology of P. mira has been systematically illustrated. Furthermore, 12 random amplified polymorphic DNA (RAPD) primers generated clear and repeatable bands among all individuals based on RAPD; 107 bands ranging from 200 bp to 2000 bp were generated with an average of 8.92 bands per primer. Thus, the RAPD technique proved to be a powerful tool to reveal variation on P. mira. This study provides comprehensive information for genetic diversity of P. mira from different altitudes.