Seed and Seedling morphology of two species of Cupressaceae – Cupressus cashmeriana Royle ex Carriéreand Cryptomeria japonica (Thunb. Ex L.f.) D. Don have been studied using light microscope (LM) and scanning electron microscope (SEM). Both the species are categorized as Near Threatened (NT) in IUCN Red List Category (2013). For characterization of seed, different parameters like shape, size, base, apex, surface were considered. For the study of seedlings, the parameters like germination pattern, root, hypocotyl, number of paracotyledons, number and nature of first leaf and subsequent leaves have been characterized. The seed and seedling characters as studied in this investigation are important as taxonomic markers for identification purpose.