Leyland cypress [×Hesperotropsis leylandii (A.B. Jacks. & Dallim.) Garland & G. Moore, Cupressaceae] is a well-known horticultural evergreen conifer in the United Kingdom, United States, Australia, New Zealand, and other countries. As demonstrated by previous studies, this taxon is a hybrid between alaska (nootka) cypress [Callitropsis nootkatensis (D. Don) Oerst. ex D.P. Little] and monterey cypress [Hesperocyparis macrocarpa (Hartw. ex Gordon) Bartel]. However, the genetic background of leyland cypress cultivars is unclear. Are they F1 or F2 hybrids or backcrosses? In this study, six individuals that represent major leyland cypress cultivars and two individuals each of its two putative parental species were collected, and three nuclear DNA regions (internal transcribed spacer, leafy and needly), three mitochondrial (mt) DNA regions (coxI, atpA, and rps3), and two chloroplast (cp) DNA regions (matK and rbcL) were sequenced and analyzed. Sequencing results of nuclear DNA regions revealed that leyland cypress cultivars consist of putative F1 and F2 hybrids as well as backcrosses. Analysis of the cp and mt DNA from six cultivars of leyland cypress revealed that their cytoplasmic (cp and mt) genomes came from alaska cypress. Our findings will provide important instructions and background knowledge on the management of these major leyland cypress cultivars as well as future studies. Meanwhile, alaska cypress and monterey cypress may have diverged with each other ≈46 million years ago. The fact that they can produce fertile hybrids indicates that hybridization events may have played an important role in the evolutionary history of the cypress family (Cupressaceae).