Aim: Integration of macroecology and palaeoecology is an important trend in understanding rapidly changing marine ecosystems. However, the spatial mismatch between these two data types has led to difficulties in interpretation, particularly for short-lived phytoplankton and their microfossils. Fronts are narrow transition zones between distinct water masses and play an essential role in partitioning phytoplankton assemblages in the ocean. Whether they also delimit microfossil assemblages deposited at the sea floor is unclear. We examined the correlation between quasi-stationary mesoscale fronts and the spatial distribution of microfossils (diatoms, dinoflagellates and silicoflagellates) in the Bohai, Yellow and East China Seas, to establish a causal link between microfossil assemblages and the factors controlling pelagic species assemblages on continental shelves. Location: China. Time period: 2003–2015. Major taxa studied: Phytoplankton. Methods: Front locations were determined using gradient analysis of monthly satellite sea surface temperature (SST) for 2003–2015. Microfossil assemblages were classified using two-way indicator species analysis of the relative abundance of 345 species collected from surface sediments at 126 sites. The relationships between frontal patterns and microfossil assemblages were evaluated by superimposing maps of front location, microfossil distribution and environmental features in the main water masses and by canonical correspondence analysis. Results: Ten major fronts and four primary microfossil assemblages were identified. Analyses of the spatial patterns of fronts, microfossil assemblages, SST, salinity and nutrients revealed that the fronts partitioned the microfossils into assemblage types corresponding to the physicochemical features of the water masses. Main conclusions: Microfossil species assemblages and their indicator species are separated by mesoscale fronts and are correlated with water properties. Producing base maps of microfossil assemblages in relationship to SST fronts enables examination of the importance of quasi-stationary mesoscale fronts in constructing microfossil patterns on continental shelves. The results displayed potential for the interpretation sediment core data and their integration with the macroecological context.