Background The conservation status of the bottlenose dolphin (Tursiops truncatus) is considered of low concern in Madeiran waters. This species of dolphin, however, is being found more frequently in the low-depth inshore area between the Madeira and Desertas islands and is subject to several threats resulting from human activities. The growing popularity of whale-watching and a rise in shipping traffic and recreational boats in the archipelago are increasing the pressure in the area. These pressures may contribute, in the medium/long term, to a negative change in the conservation status of the bottlenose dolphin. To avoid whale-watching developing to an unsustainable level, it is important to establish operating areas and designate limits on the number of tours. All the cetaceans found in the Madeira archipelago are potentially subject to the negative impacts from this activity. The precautionary principle should be considered in order to maintain or halt eventual changes to their present conservation status. The surveillance of the conservation status of cetacean species in Madeira has been conducted only in the inshore waters because of a lack of money. Therefore, there is a lack of knowledge of the offshore marine environment of the Madeira Exclusive Economic Zone. In order to fill this gap, evaluation of the potential threats (such as fisheries) to cetaceans acting in the offshore environment of the Madeira EEZ was needed. Other areas in the archipelago might also be candidates for marine Natura 2000 sites for this species. The creation of the marine Natura 2000 sites for bottlenose dolphin should take into consideration a wider perspective of the Atlantic population of the species shared by Madeira, Azores and the Canary Islands, which would clearly contribute to the improvement of the ecological coherency and connectivity of the Natura 2000 network of marine sites in the Atlantic. Objectives The CETACEOSMADEIRA II project's objectives were threefold: 1. To identify the areas of importance for the bottlenose dolphin in the coastal waters of the Madeira archipelago, with the aim of establishing adequate marine Nature 2000 sites for the species; 2. To define areas of operation for whale-watching boats in Madeiran waters and to establish the carrying capacity for this activity; and 3. To carry out surveillance of the conservation status of cetacean species in Madeira offshore waters. Results The project field work was carried out in the inshore waters (objectives 1 and 2) and offshore waters (objective 3) of the Madeira archipelago. Two different sampling methodologies were employed to achieve objectives 1 and 2. These were: the use of pre-defined zig-zig tracks randomly laid in the study area (distance sampling) - Systematic Nautical Surveys (SNS); and the use of random tracks to find bottlenose dolphin groups, mainly for photo-identification work - Random Nautical Surveys (RNS). Over the period to the end of 2012, SNS were carried out on 76 days. A total of 229 cetacean sightings of 12 different species were recorded. Over the same period, RNS were carried out on 77 days - with 199 cetacean sightings of 10 different species. Also, during the period May 2010 to December 2012, some 20 000 photographs for photo-id analysis of bottlenose dolphins were taken - with 248 new individuals added to the existing catalogue. The analysis of all the data has enabled estimates to be made of abundance, population rates, movements and population structure for the bottlenose dolphins and the short-finned pilot whales; as well as, the recording of short-term and/or long-term residency patterns for the five species studied. In addition, the survey work enabled the modelling of the distribution of some of the observed activities of the cetacean species, such as feeding, resting, socialising, calves, travelling and their reaction to boats. As a direct result of this work, the beneficiary drafted a proposal (with the accompanying scientific report) for the establishment of a Site of Community Importance (SCI) for the bottlenose dolphin in Madeira archipelago waters. The area proposed for the bottlenose dolphin encompasses the coastal waters of the islands of Madeira, Porto Santo and Desertas. The impacts of whale-watching activities on the cetaceans were also studied. These included an examination of cetacean sighting numbers vs numbers of whale-watching boats. As a result of this analysis, a proposal (and technical report) was put forward for the definition of four areas of operation for the whale-watching activities, together with certain limitations (e.g. maximum allowed number of platforms operating and maximum number of daily trips). Importantly, at the beginning of 2014 (i.e. after the project end date), both these reports were presented to the regional authorities and the first steps have been made towards their implementation. In April 2014, regional legislation has been approved establishing the limits of boats operating from different harbour clusters (equivalent to areas of operation) and maximum number of daily trips. Concerning objective 3, data collection was carried out over a total of 161 days - with 29 trips made in 10 tuna fishing vessels (i.e. covering 53% of the fleet). Ten species were identified in the (203) recorded cetacean’ sightings in the offshore waters, with the short-beaked common dolphin being the most often sighted (29%). Calves were present in 15.94% of these cetacean groups. Eight types of vessels were identified, with the tuna fishing vessels the most sighted (60.57%), and followed by cargo ships (24.23%). Plastic was the most commonly sighted type of litter in the offshore waters. These results are included in a (third) report covering the species’ abundance in offshore waters, with the main identified threats (marine traffic, interaction between fisheries and cetaceans and litter). Various public awareness raising activities were also carried out, targeting notably school children and students. These activities and results were disseminated via the website (as planned) and a Facebook page (not originally foreseen). Finally, the consequences of the project’s activities and results are already being felt, both through legislation and through the knowledge acquired that will set a reference for future comparisons in the evaluation of the conservation status of cetaceans. For example, within the reporting framework of the Habitats Directive or the Marine Strategy Framework Directive. The project resources will also continue to be used in the study and monitoring of cetaceans in Madeiran waters for conservation purposes. Further information on the project can be found in the project's layman report and After-LIFE Conservation Plan (see "Read more" section).