Genetic variations between and within 25 masson pine’s natural populations were studied in relation to their vertical and horizontal distributions in Fujian Province. Thirty-four traits were investigated and analysed, including cone and seed morphology, seedling growth, and phenology. The results suggested that there were great differences among natural populations of masson pine with vertical distributions. In both aspects, elevation populations had the same trend of variation. Variations in vertical distribution were greater than that in horizontal distribution, but sea-inland effect on the traits variations surpassed latitude and even elevation. According to the results, some suggestions were made for allocation and selection of masson pine seeds in Fujian.