Active markers tracking is performed using an innovative insect-based visual sensor. Without any optics and a field-of-view of about 60°, our novel miniature visual sensor is able to locate flickering markers (LEDs) with accuracy much greater than the one dictated by the pixel pitch. With a size of only 1cm3 and a mass of only 0.33g, the lensless sensor, called HyperCube, is dedicated to 3D motion tracking and fits perfectly with the drastic constraints imposed by micro-aerial vehicles. This small cubic position sensing device is composed of only three photosensors placed on each side of the cube, making this sensor very cheap and light. HyperCube provides the azimuth and elevation of infrared LEDs flickering at high frequency (>1kHz) with a precision of only few degrees. The simplicity, small size, low mass, and low power consumption of this optical sensor make it suitable for many applications in the field of cooperative flight of unmanned aerial vehicles, swarm robotics and more generally robotic applications requiring active beacons. Experimental results show that HyperCube provides useful angular measurements that can be used to estimate the relative position between the sensor and the infrared markers.