According to the Red List of threatened species in Croatia, Yelkouan Shearwater (Puffinus yelkouan) and Audouin´s Gull (Larus audouinii) have an unfavourable or declining status, while the Scopoli´s Shearwater (Calonectris diomedea) has a status of Near Threatened (NT). All three species are exclusively seabirds and they land on islands only for nesting. They are largely endangered by the presence of predators such as ship rats (Rattus rattus), domestic cats (Felis catus) and Javan Mongoose (Herpestes javanicus) which to a lesser extent endanger the Audouin´s Gull in the National Park Mljet. Rats are the biggest problem on some islands because they predate on eggs and chicks and because of that, the success of breeding decreases to 0%, which results in population decline and total abandonment of the colonies.

The Audouin´s Gull is also endangered by the habitat competition with Yellow-legged Gull (Larus michahellis), which breeds in much higher numbers on the islands of the Adriatic Sea. The Yellow-legged Gull is more aggressive species and begins with nesting earlier, which reduces the availability of favourable nesting locations for the Audouin´s Gull, also the predation on Audouin´s Gull has been recorded.

Bycatch during fishing with longliners is one of the biggest threats to seabirds, especially for Shearwaters. In Croatia, this threat has not yet been researched enough. There are some reports of bird bycatch, but there is not enough data to what extent it is happening. But it is not ruled out that this threat endangers the Shearwaters in the area of the Lastovo archipelago. Additionally, large exploitation of fish affects the availability of food for seabirds, especially when breeding.

Lack of data about feeding areas, roosting, wintering areas and migration greatly endangers these species. Most EU countries have designated marine Special Protection Areas (SPA), but the prerequisite for determining the Natura 2000 areas requires a good knowledge of biology and the threats of these species. Determining SPA for seabirds is an additional tool for their better protection.

The strong increase in tourist activities, cruises and boat trip near breeding sites greatly affect the success of breeding Seabirds. The ships are often too close to the colonies, and by creating noise and excessive use of light, they disturb birds and reduce breeding success.

Marine litter is one of the fastest growing global marine environmental problems. Although there is no data how marine litter impacts on seabirds in Croatia, it is expected that birds will be exposed to this problem and future research is needed.