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Knowing the abundance of a population is a crucial component to assess its conservation status and develop effective conservation plans. For most cetaceans, abundance estimation is difficult given their cryptic and mobile nature, especially when the population is small and has a transnational distribution. In the Baltic Sea, the number of harbour porpoises (Phocoena phocoena) has collapsed since the mid‐20th century and the Baltic Proper harbour porpoise is listed as Critically Endangered by the IUCN and HELCOM; however, its abundance remains unknown. Here, one of the largest ever passive acoustic monitoring studies was carried out by eight Baltic Sea nations to estimate the abundance of the Baltic Proper harbour porpoise for the first time. By logging porpoise echolocation signals at 298 stations during May 2011–April 2013, calibrating the loggers' spatial detection performance at sea, and measuring the click rate of tagged individuals, we estimated an abundance of 71–1105 individuals (95% CI, point estimate 491) during May–October within the population's proposed management border. The small abundance estimate strongly supports that the Baltic Proper harbour porpoise is facing an extremely high risk of extinction, and highlights the need for immediate and efficient conservation actions through international cooperation. It also provides a starting point in monitoring the trend of the population abundance to evaluate the effectiveness of management measures and determine its interactions with the larger neighboring Belt Sea population. Further, we offer evidence that design‐based passive acoustic monitoring can generate reliable estimates of the abundance of rare and cryptic animal populations across large spatial scales. [ABSTRACT FROM AUTHOR]

Abstract Knowledge on spatial and seasonal distribution of species is crucial when designing protected areas and implementing management actions. The Baltic Proper harbour porpoise (Phocoena phocoena) population is critically endangered, and its distribution is virtually unknown. Here, we used passive acoustic monitoring and species distribution models to describe the spatial and seasonal distribution of harbour porpoises in the Baltic Proper. Porpoise click detectors were deployed over a systematic grid of 297 stations in eight countries from April 2011 through July 2013. Generalized additive models were used to describe the monthly probability of detecting porpoise clicks as a function of spatially-referenced covariates and time. During the reproductive season, two main areas of high probability of porpoise detection were identified. One of those areas, situated on and around the offshore banks in the Baltic Proper, is clearly separated from the known distribution range of the Belt Sea population during breeding season, suggesting this is an important breeding ground for the Baltic Proper population. We commend the designation of this area as a marine protected area and recommend Baltic Sea countries to also protect areas in the southern Baltic Sea and the Hanö Bight where additional important harbour porpoise habitats were identified. Further conservation measures should be carried out based on analyses of overlap between harbour porpoise distribution and potentially harmful anthropogenic activities. Our study shows that large-scale systematic monitoring using novel techniques can give important insights on the distribution of low-density populations, and that international cooperation is pivotal when studying transnationally migratory species. Highlights • Results support the existence of a separate Baltic Proper porpoise population. • An important breeding site for the endangered Baltic Proper porpoise is identified. • Population distribution patterns give a solid base for designating protected areas. • Large-scale monitoring can give insights on distribution of low-density populations. • International cooperation is key for studies of transnationally migratory species. [ABSTRACT FROM AUTHOR]