The sampling and monitoring of nature have become an important subject due to the rapid loss of green areas. This work proposes a possible solution for a sampling method of the leaves using an ornithopter robot equipped with an onboard 94.1 g dual-arm cooperative manipulator. One hand of the robot is a scissors-type arm and the other one is a gripper to perform the collection, approximately similar to an operation by human fingers. In the move toward autonomy, a stereo camera has been added to the ornithopter to provide visual feedback for the stem, which reports the position of the cutting and grasping. The position of the stem is detected by a stereo vision processing system and the inverse kinematics of the dual-arm commands both gripper and scissors to the right position. Those trajectories are smooth and avoid any damage to the actuators. The real-time execution of the vision algorithm takes place in the lightweight main processor of the ornithopter which sends the estimated stem localization to a microcontroller board that controls the arms. The experimental results both indoors and outdoors confirmed the feasibility of this sampling method. The operation of the dual-arm manipulator is done after the perching of the system on a stem. The topic of perching has been presented in previous works and here we focus on the sampling procedure and vision/manipulator design. The flight experimentation also approves the weight of the dual-arm system for installation on the flapping-wing flying robot.