We studied the reproductive biology of the endangered species Calocedrus macrolepis. We examined flower phenology and morphology, spatial distribution of male and female cones, pollen viability, variation in pollen density around the crown, and the pollination process. Calocedrus macrolepis is monoecious with unisexual flowers on the same branches. Pollen-shed from male cones occurred from early September to mid-February, whereas the female cones were receptive from mid-September to mid-March. The inconsistency of flowering periods between male and female cones within populations and among individuals extended the pollination period. There was a layered distribution pattern of male and female cones in the crown, with more male cones in the lower layer and more female cones in the upper layer. This resulted in different selfing and outcrossing rates at various locations. The pollen of C. macrolepis lack airbags, and consequently, it was dispersed within only 10 m of the mother tree. The short pollen dispersal distance could restrict gene flow among different geographical populations. Calocedrus macrolepis is endangered because of its high degree of selfing and inbreeding resulting from its monoecious characteristics and the short distance of pollen spread. These factors may result in a population decline.