A target substance detecting apparatus includes a photonic crystal biosensor configured to include a photonic crystal, which has a reflection surface including concave portions and convex portions formed regularly on its surface, covered by a metal film, and reflecting light irradiated to the reflection surface; an optical detecting unit configured to irradiate parallel light to the reflection surface, and to detect reflected light of the parallel light reflected on the reflection surface; and a processing unit configured to obtain a wavelength at an extreme value of the reflected light detected by the optical detecting unit, and to detect at least whether the target substance is present or not based upon a shift of the obtained wavelength at the extreme value.