Artificial marking of animals for identification is frequently employed by researchers in the behavioral, biomedical, agricultural, and environmental sciences. The impact of artificial marking on experimental results is rarely explicitly considered despite evidence demonstrating that changes in phenotypic appearance can modify animal behavior and reproductive success. Here we present evidence that artificial marking of individuals within a social group has frequency-dependent effects on the behavior and physiology of domestic fowl (Gallus gallus domesticus). We demonstrate that when only 20 or 50% of individuals within a group were artificially marked, the marked birds received more aggression and had lesser body mass than the unmarked individuals within the same group. Furthermore, in groups in which only a small proportion of the individuals were marked, we report altered plasma epinephrine and dopamine levels in marked individuals. These effects of marking were imperceptible when all birds in a group were marked. This finding has important implications for animal research because, when only a subset of group members is artificially marked and used for data collection, the results obtained may not be representative of the population.