The reproductive behavior and spawning microhabitat of the flagfin shiner, Pteronotropis signipinnis, was described from aquarium observations, instream observations and microhabitat specific seining collections. Based upon aquarium observations, P. signipinnis is a broadcaster and exhibits a spawning clasp. Although spawning was never observed in nature, a high frequency of spawning related behavioral acts was observed in shallow, densely vegetated habitats (“vegetated riffles”). The spatial distribution of males and females with gonads in advanced stages of development was additional indirect evidence that vegetated riffles were an important microhabitat for reproduction. The physical characteristics of vegetated riffles may enhance the males' ability to clasp females, increase the survival of eggs and provide refuge from predation for spawning adults. Behavior related to foraging was frequently observed in “vegetated runs”, indicating that P. signipinnis relies upon different habitat types to complete its life cycle and meet its resource needs.