A review of recent literature shows that two geomorphologically different types of pockmarks, contribute to gas seepage at the seafloor. Type-1 pockmarks are defined as seafloor craters associated to fluid seepage and are the most classical type referred to as “pockmarks” in the literature. In contrast, Type-2 pockmarks reveal a complex seafloor morphology that may result from the formation/decomposition of gas hydrates in underlying sedimentary layers. Interpretation of very-high-resolution seismic data, sedimentological analyses and geotechnical measurements acquired from the Eastern Niger Submarine Delta reveal that Type-2 pockmarks are associated to the presence at depth of a conical body of massive gas hydrates. Based on acquired data, theoretical analysis and numerical modelling, it was possible to propose a novel geo-mechanical mechanism controlling the irregular seafloor deformations associated to Type-2 pockmark and to show that pockmark shapes and sizes are directly linked to the initial growth and distribution of sub-seafloor gas hydrates. The study illustrates the role of gas hydrates formation in the fracturation, deformation of the subsurface sediment and the formation of Type-2 pockmarks.