In conservation biology, a flagship species is a species chosen to raise support for biodiversity conservation in a given place or social context. Definitions have varied, but they have tended to focus on the strategic goals and the socio-economic nature of the concept, to support the marketing of a conservation effort. The species need to be popular, to work as symbols or icons, and to stimulate people to provide money or support.

Species selected since the idea was developed in 1980s include widely recognised and charismatic species like the black rhinoceros, the Bengal tiger, and the Asian elephant. Some species such as the Chesapeake blue crab and the Pemba flying fox, the former of which is locally significant to Northern America, have suited a cultural and social context. Although animal species that can be described as "charismatic megafauna" are frequently the flagship species for a protected ecosystem, large, dominant plant species sometimes serve this role as well, for example, several United States national parks, including Redwood National and State Parks, Joshua Tree National Park, and Saguaro National Park, are named for the flagship plant species for those protected areas. Butterfly species, such as the monarch butterfly, have also served as flagship species in some contexts.

Utilizing a flagship species has limitations. It can skew management and conservation priorities, which may conflict. Stakeholders may be negatively affected if the flagship species is lost. The use of a flagship may have limited effect, and the approach may not protect the species from extinction: all of the top ten charismatic groups of animal, including tigers, lions, elephants and giraffes, are endangered.

The term flagship is linked to the metaphor of representation. In its popular usage, flagships are viewed as ambassadors or icons for a conservation project or movement. The geographer Maan Barua noted that metaphors influence what people understand and how they act; that mammals are disproportionately chosen; and that biologists need to come to grips with language to improve the public's knowledge of conservation. Several definitions have been advanced for the flagship species concept and for some time there has been confusion even in the academic literature. Most of the latest definitions focus on the strategic, socio-economic, and marketing character of the concept. Some definitions are:

The flagship species concept appears to have become popular around the mid 1980s within the debate on how to prioritise species for conservation. The first widely available references to use the flagship concept applied it to both neotropical primates and African elephants and rhinos, in the mammal-centric approach that still dominates how the concept is used. The use of flagship species has been dominated by large bodied animals, especially mammals, although members of other taxonomic groups have occasionally been used.

Flagship species projects have sometimes been successful in saving the species and its habitat, as with the American bald eagle and the manatee.

Chosen flagship species are often charismatic, well-known species: see the Bengal tiger (Panthera tigris), the giant panda (Ailuropoda melanoleuca), the Golden lion tamarin (Leontopithecus rosalia), the African elephant (Loxodonta sp.) and Asian elephant (Elephas maximus). However, because flagship species are selected according to the audience they are hoping to influence, these species can also belong to traditionally uncharismatic groups if the cultural and social content is right. Less charismatic but locally significant species include the use of the Pemba flying fox as a flagship in Tanzania, and of the Chesapeake blue crab as a flagship in the US. Other examples include the use of the Ruddy Shelduck (Tadorna ferruginea) as a flagship species for the conservation of the Arjan International Wetland in Iran, where the species was selected through a participatory process involving local communities to reconnect people with the wetland's biodiversity.

Some flagship species are keystone species, like the African lion, a top predator: it used to control the populations of large herbivores, protecting ecosystems across the entire landscape. However, the lion's ability to serve as a keystone species is decreasing as its population and range decline. The WWF uses flagship species as one of its species classification categories, along with keystone and indicator species. It chooses between these when selecting a priority species to represent the conservation threats facing a certain region.