【Objective】 Chinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important, fast-growing timber species that is widely distributed in southern China. The Chenshan red-heart Chinese fir is derived from C. lanceolata originating in Jiangxi Province, and its high proportion of shiny, chestnut-brown xylem surrounding the pith is an extremely valuable raw material for craft, architecture and interior decoration. This study aimed to provide a scientific basis for the management of red-heart Chinese fir seed orchards. 【Method】 We investigated the genetic diversity and analyzed the paternity of a 1.5th generation seed orchard of red-heart Chinese fir in the Baiyunshan Mountain Forest Farm (Qingyuan District, Jiangxi Province, China). The genetic diversity of 32 parent trees and 459 open-pollinated progenies from 14 clones in a 1.5th generation clonal seed orchard was analyzed using 12 polymorphic SSR loci. We then conducted a paternity test of the progeny. 【Result】 We detected 3-7 and 4-11 alleles (N_a) at averages of 4.41 and 6.50 per SSR loci, respectively, in the parent and progeny populations. The average number of alleles in the progeny population was 2.09, which was higher than that in the parent population. The effective numbers of alleles (N_e) were 2.330 and 2.306 in the parent and progeny populations, respectively. The progeny population contained all alleles detected in the parent population. In addition, 25 alleles detected in the progeny population were undetectable in the parent population. The Shannon information index (I) was 1.004 and 0.992 in the parent and progeny populations, respectively, indicating slightly higher genetic diversity in the progeny than in the parent population. The observed heterozygosity (H_o) was smaller in the progeny, than in the parent population (0.525 vs. 0.571), indicating a slightly lower proportion of heterozygosity in the progeny than in the parents. The multilocus (t_m) and single-locus (t_s) outcrossing rates in the seed orchard were 1.012 and 0.991, respectively, and the inbreeding between parents was not significant (t_m-t_s = 0.021). The number of effective pollen donors (N_ep) was 7.81. The multilocus [R_p(m)] and single locus [R_p(s)] paternal correlations of the seed orchard were 0.128 and -0.016, respectively. The difference [R_p(s)-R_p(m)] between them was -0.144 < 0, indicating the absence of close relationships among the parents. The multilocus outcrossing rate (t_m) among families ranged from 0.938 to 1.200, and the multilocus outcrossing rate (t_m) of 10 families was more than 0. The biparental inbreeding (t_m-t_s) among families ranged from -0.127 to 0.150, and the t_m-t_s of nine families was more than 0, indicating that these families were inbred. The male parents of 325 progeny were determined at an 80% confidence level, accounting for 70.8% of the total progeny analyzed. The male and female parents of all progeny were generated from different clones, indicating the absence of selfing in this seed orchard. The proportions of paternal identification among families differed. The proportion of paternal identification of family No. 41 was the highest (93.9%), whereas that of the other families ranged from 54.3% to 90.9%. Paternal parents of 30 offspring in family No. 8 were identified, the paternity of 16 offspring was the same clone, accounting for 53.3% of the total offspring of this family. Paternal parents of 26 offspring in family No. 12 were identified, the paternity of 12 offspring was the same clone, accounting for 46.2% of the total offspring of this family. These results indicated that pollination affinity differed among the clones. A non-random mating phenomenon was also identified in the seed orchard. Among 32 clones, 26 provided effective pollen. Clone numbers 22 and 29 provided pollen for 33 offspring with the highest male parent contribution rate of 10.2%, compared with the 0.3%-8.9% rate of other clones. Eleven clones with the highest paternal contribution produced 70.2% of the offspring. 【Conclusion】 The 1.5th generation clonal seed orchard of red-heart Chinese fir was found to have rich genetic diversity, which remained equally in the progeny and parent populations. The outcrossing rate of this seed orchard was high, and some families had a low level of inbreeding. Self-pollination was absent, pollination affinity differed among clones, and the paternal contribution of clones was not equal throughout this red-heart Chinese fir seed orchard.