Phanagoria – the largest known ancient Greek settlement on the territory of Russia is situated on the Taman peninsula on the southern side of the Taman bay. The unique feature of the site is that about 1/3 of the settlement of Phanagoria is currently flooded by waters of the Taman bay due to the transgression of the Black sea level since antiquity. In 2012 in the course of underwater prospection of the Taman bay a wooden ship buried under the 1.5 m thick bottom sediments was discovered <i>in situ</i>. The unique feature of the ship is excellent preservation of its wooden parts, which makes it one of the few finds of this kind ever made on the territory of Russia. This paper presents a case-study of application of photogrammetry technique for archaeological field documentation record in course of underwater excavations of the Phanagorian shipwreck. The advantages and possible underwaterspecific constraints of automated point cloud extraction algorithm which was used in the research are discussed. The paper gives an overview of the practical aspects of the workflow of photgrammetry technique application at the excavation ground: photo capture procedure and measurement of control points. Finally a resulting 3-D model of the shipwreck is presented and high potential of automated point cloud extraction algorithms for archaeological documentation record is concluded.