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ABSTRACT Aim Climate change could result in an increase in species richness because large-scale biogeography suggests that more species could be gained from equatorial regions than may be lost pole-ward. However, the colonization of newly available habitat may lag behind the rate dictated by climatic warming if there exists of a lack of connectivity between 'donor' and receiving areas. The objective of this study was to compare how regional warming affected the biodiversity of marine fish in areas that differed in their connectivity in the Baltic Sea. Location North-east Atlantic, Kattegat and Baltic Sea. Methods The total species richness and the mean species richness from scientific surveys were related to changes in temperature and salinity. Changes in the extent of the distribution of individual fish species were related to the latitudinal distribution, salinity tolerance, maximum body size and exploitation status to assess to what extent climate change and fishing impacts could explain changes in species richness in the Baltic. Results Rising temperatures in the well-connected Kattegat correlated to an increase in the species richness of fish, due to an increase in low-latitude species. Unexpectedly, species richness in the poorly connected Baltic Sea also increased. However, the increase seems to be related to higher salinity rather than temperature and there was no influx of low-latitude species. Main conclusions These results do not support the hypothesis that low-connectivity areas are less likely to see increases in species richness in response to warming. This indicates that the effect of climate change on biodiversity may be more difficult to predict in areas of low connectivity than in well-connected areas. [ABSTRACT FROM AUTHOR]