Sedimentary coastal ecosystems like the European Wadden Sea in the northeastern Atlantic harbor large populations of burrowing infauna, such as arenicolide polychaetes. These 'ecosystem engineering' macrofaunal organisms destabilize sediments by reworking and irrigating them, leading to a reorganization of sediment physicochemical state and bacterial communities. Here, we tested the effects of the lugworm Arenicola marina on intertidal psammophilic protistan community diversity and structure in a field experiment. We applied pyrosequencing and community structure analyses to samples in which we manipulated lugworm densities. Irrespective of the presence or absence of the lugworm, protistan abundance and diversity (mostly diatoms and ciliates) was higher in oxic surface sediments compared to anoxic subsurface sediments. In the presence of A. marina, protistan abundances and diversity decreased decisively in surface as well as in subsurface bulk sediment. Also, the protistan community composition differed remarkably, with only 28% of all phylotypes (n total = 855) shared between habitats with and without lugworms. Twenty-seven percent of all taxa were detected exclusively in the presence of lugworms, and 62% of the taxa found in the oxic subsurface sediment surrounding the lugworm burrow were limited to this distinct microenvironment. This suggests that lugworm burrows provide an ecological niche potentially hosting protist taxa that are adapted to fluctuating oxygen supply. We conclude that though the activities of A. marina reduce the overall abundance of protists, they select for very specific and well-adapted taxa. This adds to the overall protistan diversity in intertidal sandflats on larger spatial scales. Most likely, the observed effects of lugworms on protistan community structure and composition are due to a combination of direct trophic and indirect sediment- mediated effects, such as disturbance by reworking the sediment, oxygen supply by burrow ventilation and increased pore water exchange due to bioadvection. © Inter-Research 2012.