Because of their small size and fragility, larvae of many amphibian species are difficult to mark unambiguously for experimental studies. This constraint limits our ability to run experiments in which individual interactions matter and so limits our ability to study how social behaviors affect individual fitness. We anesthetized small (<8 mm long) Cane Toad (Rhinella marina) tadpoles and used a biopsy punch to remove tissue from either the dorsal or ventral tail fin, enabling the identification of several cohorts within an enclosed system. The tail fin clips remained readable for >30 days and had only minimal effects on tadpole growth, survival, and swimming performance. Marking the membrane of a tadpole tail fin provides a cost-effective method for cohort marking with minimal equipment and training. It also provides the opportunity to gather extra data on an individual (such as DNA) with minimal further stress to the animal.