During the past four decades several viral diseases have been detected in seals and cetaceans inhabiting the waters of Northern Europe. Viruses such as porpoise morbillivirus (PMV) and the novel phocoena pestivirus (PhoPeV) are detected occasionally with yet unknown impacts on the population health. In contrast, outbreaks of phocine distemper virus (PDV) in 1988 and 2002 and influenza A (IAV) in 2014 have caused significant population fluctuations in the harbour seals. This project sought to i) investigate the presence of influenza and morbillivirus in seals and harbour porpoises of the Baltic Sea-North Sea region, ii) elucidate the viral distribution of PhoPeV in the same region and iii) broaden the understanding of distemper emergence and evolution in the marine environment. Investigations on viral presence were conducted based on qRT-PCR screenings of lung tissue and tracheal swaps collected from a total of 99 harbour seals, 126 grey seals, 73 ringed seals and 78 harbour porpoises in the Baltic Sea-North Sea region between 2002-2019. We did not find any evidence of morbillivirus and IAV infections outside of the outbreaks in 2002 and 2014, but occasional spillover from Arctic seals and avian reservoirs has previously been reported. As both PDV and IAV outbreaks spread from central Kattegat which geographically connects Baltic and North Sea populations, it is suggested to increase pathogen surveys in this region. PhoPeV was detected in a Belt Sea harbour porpoise expanding the distribution range of the virus from the North Sea to the Baltic region. Phylogenetic analyses found the novel sequence to be closely related to genotype 1 North Sea sequences with a recent divergence between 2007-2011. While still poorly understood PhoPeV may impact the reproductivity of harbour porpoises and we advocate that future surveys include the virus in their analyses. Bayesian phylogenetic analyses of PDV and canine distemper virus (CDV) points to a 17 th century divergence between the two viruses. Based on the mapped distemper distribution, broad host range and basal placement of terrestrial morbilliviruses a CDV-like ancestor was suggested to have given rise to PDV in the North Atlantic. The combined work presented in this thesis provides valuable insight to the emergence and circulation of morbillivirus, IAV and PhoPeV in North European seals and harbour porpoises relevant to future monitoring efforts.