The zebrafish is increasingly utilized in behavioral brain research, as it offers a useful compromise between system complexity and practical simplicity. However, a potential drawback of this species in behavioral research is that individuals are difficult to distinguish. Here we describe a simple marking procedure, subcutaneous injection of color dyes, that may alleviate this problem. The procedure allowed us to successfully mark zebrafish and distinguish them for a period of more than 30 days, which is sufficiently long for most behavioral paradigms developed for this species. In addition, we also provide data suggesting that the injection-based marking does not significantly alter social interaction, as defined by the frequency of agonistic behaviors within shoals.