Biodiversity monitoring, essential to detect impacts of natural and anthropogenic changes on marine ecosystems, is costly, time-consuming and requires high taxonomic expertise. Taxonomic surrogacy might be a solution to overcome these problems and accurately reflect species-level community patterns, but its efficiency has mainly been assessed as taxonomic sufficiency and rarely from long-term monitoring data. Here, the efficiency of subset taxa (i.e. Polychaeta, Crustacea and Mollusca) for summarizing long-term community dynamics was tested in different coastal habitats. The data set came from a yearly long-term macrobenthic monitoring programme (2007-2019) in western France, in 2 biogenic and 2 bare habitats. Community trajectory analysis (CTA), a statistical approach allowing for quantitative measures and comparisons of temporal trajectories, was used to test for similitudes between overall community, subset-taxa and non-subset-taxa dynamics. Polychaeta best reflected the spatial diversity of the different sites as well as the temporal dynamics of the non-Polychaeta species, with more efficiency in biogenic compared to bare habitats. Our study confirmed that the subset-taxon method may reflect long-term benthic habitat dynamics and that CTA is an effective tool to test their efficiency.