Abstract: Phoebe zhennan is a precious and unique timber species in China. The establishment of a core collection have important value for the strengthen of resources protection and utilization, and speed up the breeding process of P. zhennan. Taking 102 germplasms of P. zhennan as materials. The methods of maximization strategy (M strategy), random sampling, simulated annealing algorithm maximizing the genetic diversity, and simulated annealing algorithm maximizing the number of alleles were used to construct the core collections using 14 SSR primers. The results showed that 166 alleles were detected by 14 SSR primers, and the average of the effective alleles was 4.875. The Shannon’s information index was 1.297, indicated relative high genetic diversity in the germplasms of P. zhennan. Comparative analysis showed that the core collections with relative high sampling proportion of constructed by maximization strategy, simulated annealing algorithm maximizing the genetic diversity, and simulated annealing algorithm maximizing the number of alleles were all showed high representativeness. The retention of alleles in core collections that constructed by simulated annealing algorithm maximizing the number of alleles and maximization strategy were all reached 100.00%, but the retention of the effective alleles and genetic diversity in core collection that constructed by algorithm maximizing the number of alleles were lower than maximization strategy. There was no obviously difference of the retention of Shannon’s information index in core collections that constructed by simulated annealing algorithm maximizing the genetic diversity and maximization strategy, but the alleles and effective alleles in core collection that constructed by maximization strategy were higher than simulated annealing algorithm maximizing the genetic diversity. Therefore, maximization strategy was the best sampling strategy in core collection construction according to the genetic diversity parameters. The principal coordinate analysis also showed that the core collection could represent the genetic diversity of the origin collection. The 60 germplasms includes 58.8% of the all germplasms, the retention of alleles, effective alleles, and Shannon’s information index were 100.00%, 120.51%, and 106.86%. Specific molecular identity for 60 core collections were established by the bands of 14 SSR primers, which could accurately identification the core collections. Our results provided theoretical basis and core materials for further research, utilization, and excellent gene resource mining of P. zhennan germplasms.