The especial feature of high-latitude marine routes is unusual geodynamic regime of the sea bed and hydrodynamic of waters, caused by a wide spread of a submarine permafrost, enriched with methane gas-hydrates. They had been accumulated during the Ice Age, and after deglaciation the both permafrost and gas-hydrates are subject to destruction, accompanied by a runoff of methane into sea water and atmosphere. There are two mechanisms of degassing: diffusion (DDG) and flare-bubble (FDG). DDG acts permanently resulting in appearance of areas with an abnormal concentration of methane dissolved in water, decreasing its density, and so affecting a floatability of vessels. FDG appears locally and impulsively, but this type of degassing presents an essential risk for a safety of high-latitude transport communications, as well as for underwater technical infrastructure in the exploited oil and gas fields. Fast-growing gas-hydrate pingoes can change the bottom relief and generate newborn islands or shallow banks with hummock. Consequences of the blowing up of subaqueous pingoes are very hazardous, and include a formation of giant pockmarks and craters at the sea bed, an emergence of large methane bubbles to the sea surface and emission in air of the methane tails up to a thousand kilometers in length. The entry of ships into the FDG zone is fraught with flooding; the engineering facilities in these zones will be subjected to mechanical damage and fires. Due to provide both industrial and ecological safety the special preventive measures are needed.