We studied how habitat selection influences the distribution and densities of a stenotypic yellowcheek darter Etheostoma moorei (Raney and Suttkus) and eurytypic rainbow darter E. caeruleum (Storer) in a headwater stream subjected to periodic drying. We spatially sampled in habitats within riffle substrates and at four sites four to six times per year in the Middle Fork of the Little Red River. Yellowcheek darters were associated with cobble and gravel more than rainbow darters. Rainbow darters moved along the substrate surface and positioned themselves further downstream in riffles, whereas yellowcheek darters occurred further upstream in or near crevices between gravel and cobble. Neither species was found in the hyporheic zone during riffle drying. The rainbow darters used pools during riffle drying but not yellowcheek darters, which could explain recolonization of previously dry upstream sites by rainbow darters but not yellowcheek darters. Rainbow darters were at their greatest densities in upstream riffles where yellowcheek darters had not recolonized, suggesting niche partitioning. These temporal differences in microhabitat selection appear to enable the coexistence of these two sympatric and ecologically similar darters.