To overcome costs and logistical constraints associated with capturing and marking a sufficient number of elk (Cervus elaphus) for population estimation, elk are sometimes marked with paintballs fired from a helicopter flying overhead. Although marking elk with paintballs is a cost-effective marking technique, there are some unique aspects of this method that may bias population estimates. When analyzing the mark–recapture data, the assumption that each animal has an independent and identical probability of being marked and resighted may be violated. Instead, the probabilities of marking and resighting are likely to be a function of herd size. We explored the potential biases of paintball, mark–resight surveys of elk and present alternative methods that could be used to generate population estimates from mark–resight data, including Bailey's binomial MLE, cluster sampling, and bootstrap methods. Our results suggest that population estimates will generally be negatively biased; the magnitude of the bias depends upon the degree of herd aggregation and fidelity. To minimize these biases, we recommend (1) marking animals when they occur in many small herds, (2) marking equal proportions of individuals in each herd, and (3) determining the degree of aggregation and fidelity of elk to herds in each area. Although these recommendations do not facilitate the primary goal of the technique (i.e., the ability to mark numerous animals easily), following them will provide more reliable population estimates.