An atmosphere sampling system includes: an unmanned rotary-wing aircraft platform including: an airframe capable of lifting a selected payload mass; at least one motorized rotor; and, a flight control system including an on-board controller; an atmosphere sampling unit having a total mass no greater than the selected payload mass, and including: a blower preferably having backward-facing blades, an inlet structure to draw in air to be sampled, and an outlet to discharge air after sampling; a plurality of sample containers; and, an indexing mechanism to move selected sample containers, one at a time, into contact with the inlet structure so that samples may be collected; and, a power supply with sufficient capacity to operate the motorized rotor(s), the onboard portion of the flight controller, the blower, and the indexing system.