Polyaigos hosts rare species of plants, such as the single blossom orchid (Serapias carica var. monantha) and many Greek endemic species. In general, the flora of the island varies from brushwood to shrubs, such as the common juniper and the wild olive tree.
Its fauna is significant as well. It hosts rare or endangered endemic species, such as the Mediterranean monk seal Monachus monachus, the endemic viper Microvipera schweizeri (it lives only in Kimolos, Polyaigos, Milos and Sifnos), the endemic blue lizard Phdarcis milensis, the falcon Falco eleonore (Eleonora’s falcon), the Bonelli’s Eagle and more. Due to its great ecological significance Polyaigos has been integrated in the Network Natura 2000 as a Site of Community Importance.