It is often postulated that natural systems are expected to suffer an increasing risk of infectious disease outbreaks as climate change accelerates. In the northern Argentine Sea, the rise of ocean temperature has produced a tropicalization of demersal megafauna since 2013. This rapidly warming hotspot provides an excellent model to test whether fish parasites have increased, declined, or remained stable in the region. Cardiocephaloides physalis a parasite of penguins Spheniscus magellanicus as adult and suspected to parasitize anchovies Engraulis anchoita as larvae is here used to compare their occurrence and abundance between samples composed by 1752 fish of variable age caught at different latitudes during 1993–1995 and 2022 and between 20 juvenile birds and literature data. In the present work, the identity of metacercariae as C. physalis is confirmed genetically, as well as a net decline of population parameters of the parasite to its effective disappearance in anchovies from northern areas and to extremely low levels in fish from southern regions and penguins. After analysing possible causes for such changes in a scenario of rapid regional tropicalization, a direct effect of increasing temperature on parasites arose as the main causal candidate for the observed decline in their populations over the last decades. Beyond the biological and ecological consequences of global change on them, parasites offer excellent systems for measuring and monitoring such effects. The almost local extinction of C. physalis in a marine hotspot of global warming seems to be one of the first examples of such processes.