To improve the ecological and economic benefits of Korean pine (Pinus koraiensis), we analysed and evaluated its germplasm resources. This promotes in-depth research and utilisation of germplasm resources, providing excellent genetic resources for Korean pine breeding. We performed genetic analysis based on morphological and physiological traits and nuclear SSR molecular marker data was performed by collecting 314 clones (5 ramets of each clone) of Korean pine from eight (8) locations within the Korean pine range. The core collection underwent testing and evaluation for representativeness using variable rate (VR), coincidence rate (CR), variance difference percentage (VD), mean difference percentage (MD), Shannon index (I), and other indicators. The results indicated significant differences in morphological and physiological traits among the populations. All traits had a coefficient of variation (CV) greater than 10%, except for the water content of the needles (WC), which had an average CV of 17.636%. The populations showed high overall genetic diversity, with the HL (Helong) population exhibiting the highest genetic diversity, with an Ne (number of effective alleles), I, and He (expected heterozygosity) of 3.171, 1.103, and 0.528, respectively. Genetic variation mainly originated from individuals within populations, while the variation between populations was relatively small, at only 3%. The population did not exhibit any distinct subpopulation structures and was mainly derived from two admixed gene pools. Six core sets were obtained using different sampling strategies, and subset 6 was identified as the core collection, consisting of 114 individuals, representing a selection rate of 36.31%. In conclusion, the most appropriate method for constructing the core collection of Korean pines is the M-strategy (maximizing the number of alleles), based on both phenotypic and molecular data. The resulting core collection effectively represents the genetic diversity of the entire population effectively.