Pinus koraiensis is a rare and protected species in China. In this study, our objectives were to determine the phenotypic variation, distribution mechanisms and patterns of different P. koraiensis populations in a seed orchard. We studied morphological variation among and within six populations of P. koraiensis based on analysis of 15 phenotypic traits (including needle, cone, and seed traits). Nested analysis of variance, coefficient of variation, multi-comparison, and the unweighted pair-group method with arithmetic means (UPGMA) cluster analysis were used to analyse the data. The results showed that:(1) there were significant differences in all 15 traits among and within populations of P. koraiensis, revealing a large variation. Within the genus Pinus, P. koraiensis shows intermediate levels of variation. The most southern population showed the highest mean value in 10 of the 15 traits; (2) mean phenotypic differentiation coefficient (Vst) within populations was 87.61%, higher than that among population (12.39%), indicating that the largest part of phenotypic variation is retained within populations in P. koraiensis; (3) the average value of coefficient of variation (CV) was 13.28%, and ranged from 6.16% to 31.48% among traits. Among traits, the CV decreased from cone (17.86%) to needle (11.19%) to seed traits (9.87%), which were the most stable traits. The phenotypic diversity of DL and FL populations was higher than that of other populations; (4) according to UPGMA cluster analysis, the phenotypic traits of P. koraiensis populations clustered by geographical distance. The six populations P. koraiensis used in this study can be divided into four groups, which are significantly related in topography (mountains in northeast of China). Overall, we observed abundant phenotypic variation among and within populations, which provides critical information for resource collection, conservation, and breeding of this ecologically important species.