Whale-watching tourism in Ecuador thrives through the spectacular image of a flagship species, the humpback whale. Seemingly, it is an example of an industry regulated and managed in accordance with sustainable principles of nature conservation, thanks to the work of Ecuadorian scientists who advocate for policies to protect whales from harmful exploitation. However, does the use of the whale as an icon of conservation result in its utilization as a mere commodity for profit? Through ethnographic fieldwork including interviews, observations, and textual analysis, it is shown that the Ecuadorian practices of whale conservation have resulted in the whale becoming a subject of governance, by which the wild animals are recognized as entities worthy of ethical treatment. Using the humpback whale as a flagship species, the Ecuadorian scientists practice biopolitics through the strategies of categorizing, monitoring, and regulating human interactions with the whale population. The success of this approach to wildlife governance highlights the role of NGO-affiliated scientists as knowledge producers and policy advocates.