In Japan, pollen from Japanese cedar (Cryptomeria japonica) and Japanese cypress (Chamaecyparis obtusa), species that have been planted in approximately 4.5 and 2.6 million ha, respectively, is spread wide through aerial dispersion in spring. Consequently, Japanese cedar/cypress pollinosis (JCCP) is the major phenotype of allergic rhinitis (AR) in Japan, and significantly impairs the quality of life (QOL). Compared with Japanese cedar pollinosis, the pathogenesis and management of Japanese cypress pollinosis remain unclear. Cha o 1 and Cha o 2 are major allergens in Japanese cypress pollen, and have considerable homology with Cry j 1 and Cry j 2, respectively, in Japanese cedar pollen. Several other components were recently identified in Japanese cypress pollen, and may facilitate allergic inflammation via IgE-independent mechanisms. Allergen-specific CD4+Th2 cells producing interleukin (IL)-4, IL-5, IL-13 and IL-31 are believed to play central roles in the pathogenesis of AR. The major human T cell epitopes in Cha o 1 and Cha o 2 have been identified. Compared with those in Cry j 1 and Cry j 2, both common and unique T cell epitopes in the cypress allergens have been characterized. Peripheral blood mononuclear cells (PBMCs) produced these Th2-type cytokines in response to a crude extract of Japanese cypress pollen. Among these cytokines, induction of antigen-specific IL-5 and IL-31 production is closely associated with the onset and exacerbation of Japanese cypress pollinosis, respectively. Allergen-specific immunotherapy using a standardized extract of Japanese cedar pollen is effective in controlling both naso-ocular symptoms and QOL during the period of cedar pollen dispersion, although the significant efficacy tends to be reduced during the period of cypress pollen dispersion, especially when the pollen dispersion is high. IL-5 production by PBMCs in response to the crude extract of Japanese cypress pollen did not differ significantly between patients with and without the immunotherapy, suggesting that unique component(s) in Japanese cypress pollen can induce IL-5 production, which is not fully suppressed by immunotherapy with the standardized extract of cedar pollen. The Practical Guideline for Management of Allergic Rhinitis in Japan recommends that patients who experience severe symptoms of pollinosis every year should receive early interventional treatment. Although early interventional treatment with a histamine H1 receptor antagonist (H1RA) is effective for Japanese cedar pollinosis, especially at the beginning of the season, this treatment has limitations for Japanese cypress pollinosis when exposure to the pollen is high. Combined therapy with a leukotriene receptor antagonist and/or intranasal corticosteroids may be required to fully control the worsening of JCCP during the cypress pollen season.