Besides the traditional image and video systems, metho-dologies and technologies for the acquisition of stereoscopic images are becoming simple and effective instruments for reconstructing the three-dimensional (3D) model of the investigated scene. Differently from the traditional 2D images, 3D models provide an accurate geometry of the framed scene, where distance, size and volume of the observed subjects can be automatically estimated. This paper presents a low cost stereo system for autonomous underwater imaging aimed at the comprehensive analysis of underwater organisms, benthos, and zooplankton through the investigation of reconstructed 3D models of the framed targets. In order to overcome the tight constraints given by the high cost of commercial underwater stereoscopic devices and the high probability of losing these devices during deployments, the proposed system was developed as autonomous, low cost and with the smallest possible size, in order to be easily deployed both on fixed and mobile platforms (e.g. submerged stations, oceanographic moorings, floats, drifters, and AUVs).