The major threats facing Monk Seals are:
- Destruction of habitat and habitat exclusion: Monk seals originally used to inhabit sandy coastlines and islands. However, due to the extensive use of the sea and seaside, they now hide in sea caves. Human encroachment and human pressures are reducing the available habitat for monk seals and further isolating pockets of this already fragmented species.
- Mass tourism and human disturbance: Human access to natural habitat areas, curious tourists, and unscrupulous diving guides disturb the seals and hamper their reproduction. Mass tourism has had a significant impact on this already declining species.
- Inadequacy of their new habitats: Females are forced to pup in relatively undisturbed areas (the sea caves), but these are particularly exposed to rough waves and bad weather conditions. This situation threatens the survival of baby seals, which may be swept away from their birth caves and injured or drowned during storms.
- Coastal and sea pollution: The increasing intensity of maritime traffic and the consequent increase in pollution of the marine environment can endanger seals and even reduce fish stocks. Pollutants enter the sea through dumping from ships or from land-based activities, maritime accidents and domestic or agricultural run-off.
- Decreased food availability: Food resources for the monk seal have been reduced by the extension of costal fishing areas. The depletion of fish stocks can lead to a lack of sufficient food for seals and reduction in their physical condition and breeding success.
- Incidental capture in fishing gear: Pups are endangered by fishing nets set near their birth caves - they risk entanglement and drowning. The increase in coastal fisheries and use of new fishing techniques can make the sea more dangerous for seals, partly because they are very curious animals.
- Deliberate killings by traditional fishermen: Traditional fishermen have been known to consider adult seals as pests and as competitors for increasingly scarce resources. Although it is strictly forbidden, monk seals are still sometimes dynamited or shot.
- Disease and toxic algae: Biotoxins are fatal poisons leading to massive mortality. Biotooxins paralyze seals when they dive, which makes them sink. Viruses and parasites may also cause serious epidemic episodes.
- Genetic depression: Monk seals have a very low genetic variability. Distances are so great between the Mediterranean and Atlantic populations' locations, that genetic flow is highly unlikely.












