Increasing prevalence of pollen allergies has raised concerns about human health. Development of a facile and precise method to detect pollen allergens would thus be of significance for environmental assessments and medical diagnoses. Here we report a sensitive colorimetric method to detect the Japanese cedar pollen allergen, Cry j 2. The method consists of two steps: a signal amplification based on the catalytic DNA hairpin self-assembly, followed by a signal transduction using the salt-induced non-crosslinking aggregation of gold nanoparticles densely modified with short DNA. The assay exhibits a detection limit of 0.2 ng/mL, which is 130-fold greater than that of the previously reported one. Moreover, the assay enables the detection of Cry j 2 spiked in soil solutions by avoiding any interference from the contaminants. The signal amplification system includes an anti-Cry j 2 DNA aptamer, which accounts for the absence of false responses to five non-target allergen proteins. The present method could be of general applicability to various proteins by using appropriate aptamers.