Genomic data have revealed that kelp rafts travel across oceans, acting as ‘taxis’ that transport animal passengers between distant Southern Hemisphere coastal ecosystems, including traversing Southern Ocean fronts to reach Antarctica. New findings suggest, however, that not all passengers are benign; pathogens are also rafting with kelp, and can jump hosts to infect endemic species. Disease-like symptoms are appearing on iconic, ecologically and economically important kelp species in Aotearoa (New Zealand), and while some disease agents have been identified (such as the protistan pathogen Maullinia), in most cases we don’t know what is causing symptoms. Disease outbreaks have the potential to wreak havoc on ecosystems, destabilising food webs and removing critical habitat for fish and shellfish. Using RNA sequencing, our preliminary research has revealed that several new virus strains are associated with ‘sick’ kelp in Aotearoa. Furthermore, surveys of sites along the south-eastern coasts indicate some possible links between symptoms and pollution; for example, there is positive a correlation between how near a site is to a sewage outflow, and how unhealthy kelp appear to be. Interdisciplinary research that combines genomic data with ecological data and environmental modelling is needed if we are to understand and manage the causes, consequences and connectivity of disease agents affecting foundational kelp species.