Random amplified polymorphic DNA (RAPD) and single-strand conformation polymorphism (SSCP) analyses were employed for investigating genetic relationships of three Athrotaxis D.Don species. Twenty-nine RAPD primers produced 103 polymorphic bands. Principal component analysis revealed the genomic differentiation among three Athrotaxis species. Mean genetic distance (mean d) between A. selaginoides D.Don and A. cupressoides D.Don was 0.89. Mean d values were reduced to 0.42/0.54 between A. laxifolia Hook. and A. selaginoides/A. cupressoides, respectively. Intraspecific mean d of A. selaginoides and A. cupressoides were, respectively, 0.03 and 0.11. These values indicated that A. laxifolia, which is regarded as a hybrid between A. selaginoides and A. cupressoides, is genetically intermediate between A. selaginoides and A. cupressoides. This genetic characteristic and previously reported morphological characteristics suggest the hybrid origins of A. laxifolia. The genomic composition of A. laxifolia was estimated by the number of bands specific to A. selaginoides or A. cupressoides in order to determine the genomic contribution of these two species to its proposed hybrid, A. laxifolia. All of the five individuals investigated herein possessed genomes derived almost evenly from A. selaginoides and A. cupressoides. Furthermore, the pollen donor of A. laxifolia was determined by SSCP analysis of the atpA gene on chloroplast DNA. Because all of the five A. laxifolia possessed the A. selaginoides-type chloroplast genome, A. laxifolia would be a hybrid of A. selaginoides as a paternal parent and A. cupressoides as a maternal parent.