A molecular detection apparatus, comprising: a chamber; a light source provided in the chamber and configured to emit light; a detector including at least one sensor and configured to generate a first detection data and a second detection data, the sensor being provided in the chamber and being configured to capture molecules of target molecules, the first detection data corresponding to the number of captured molecules per predetermined time under a first emission condition of the light, and the second detection data corresponding to the number of captured molecules per predetermined time under a second emission condition of the light; and a discriminator to discriminate the target molecules using the first and second detection data.