Abstract: In this study, 5 plots (A₁, A₂, K, H₁, H₂) of 18–24 years old red pine primary seed orchard were used as research materials, and growth index investigation and molecular marker analysis were used as selection methods to screen the second generation of red pine trees. The results of growth traits analysis showed that 94 excellent individual plants of red pine were selected with an average selection rate of 0.789% based on the odds ratio of individual tree volume ≥1.80. In the A₁ plot, the average tree height was 6.97 m, the average DBH was 17.81 cm, and the average tree volume was 0.092 m³. Five excellent individual plants were selected, and the selection rate was 0.667%. In the A₂ plot, the average tree height was 9.18 m, the average DBH was 18.24 cm, the average tree volume was 0.119 m³, and 27 excellent trees were selected, the selection rate was 2.368%. In plot K, the average tree height was 10.75 m, the average DBH was 18.65 cm, and the average tree volume was 0.135 m³. Three excellent trees were selected, and the selection rate was 0.213%. In H₁ plot, the average tree height was 5.76 m, the average DBH was 12.77 cm, and the average tree volume was 0.04 m³. Twenty-six excellent trees were selected, and the selection rate was 0.303%. H₂ plot average tree height 5.9 m, average DBH 11.15 cm, average tree volume 0.031 m³, 32 excellent individual plants, the selection rate of 0.382%. The results of SSR analysis showed that 294 alleles were detected in 13 SSR loci, indicating a high level of genetic diversity. Under the similarity coefficient of 0.947, 94 individual plants could be divided into 74 homologous groups.In order to effectively control inbreeding, 74 excellent single plants were selected from homologous groups and used as garden materials for the second generation of red pine seed orchard.