A molecular detection apparatus according to an embodiment includes: a collection unit collecting a detection target gas containing a molecule to be detected; a substitution unit substituting a part of a molecular structure of at least a part of the molecule to generate a substitution product; a detector including a plurality of detection cells each having a sensor unit and an organic probe disposed at the sensor unit, the organic probe capturing the molecule or the substitution product; and a discriminator discriminating the molecule by a signal pattern based on an intensity difference of detection signals generated with the molecule or the substitution product being captured by the organic probes of the plurality of detection cells.