We present a new method for measuring low concentrations and simultaneously small volumes of fluorescent molecules based on the use of the Ebbesen effect of the extraordinary transmission (EOT) of light through an array of nano-holes. In the method the EOT effect is realized at the fluorescence wavelength of the detected molecules with a low transmission of light at the absorption wavelength. The approach allows realizing high level of the sensor sensitivity due to suppression of the inevitable parasitic luminescence of the sensor substrate. The method was demonstrated by detecting an ultra low concentration (at a level of 20 pg/ml (3 p.p.t.)) and an ultra-small volume (about 5 {\mu}l) of Cy-5 fluorescent markers in a dimethyl sulfoxide solution.
