An assemblage of microbial endoliths is described from echinoderm and trilobite skeletal grains in limestones from the Lower Ordovician (Arenig‐Llanvirn) of northern Estonia. The different morphologies indicate that the largest structures, both straight and branched (2–8 μn in diameter), belong to autotrophic organisms, most probably cyanobacteria or algae, whilst thinner forms belong to saprotrophic fungi. The occurrence of described endolithic autotrophic assemblage suggests photic conditions at the sediment‐water interface and may confirm low sedimentation rate or even nondeposition at the transition between Lower and Middle Ordovician in northern Estonia.