Sensing pollen allergens is required to prevent allergic disorders such as pollinosis. Aptamers, which bind to specific molecules, offer great potential as useful tools for detecting pollen allergens as measures against allergic disorders. Here, we report the identification of DNA aptamers binding to Cry j 2, one of the major allergens in Japanese cedar pollen, and the histochemical sensing of Cry j 2 in ruptured Japanese cedar pollen. DNA aptamers were selected by systematic evolution of ligands by exponential enrichment (SELEX) using nitrocellulose membranes. Through four rounds of SELEX, we identified aptamers binding to Cry j 2. The aptamers generated staining in ruptured Japanese cedar pollen on glass slides without extraction, similar to anti-Cry j 2 antibodies. The staining was compatible with starch localization, in which Cry j 2 is present. An aptamer, CJ2-06, which had high and specific binding ability to Cry j 2 (K(d)=24 nM), detected an amount of Cry j 2 equivalent to that in several tens of micrograms of pollen. Cry j 2 contained in house dust was detected in a spike test. The aptamers identified in this study can be powerful tools for allergen recognition in the practical biosensing of Cry j 2, leading to preventive measures against allergic disorders caused by Japanese cedar pollen.