With regards to flora, the territory is home to 69 taxa of endemic vascular plants: 15 are exclusive to Porto Santo (Crepis noronhaea, Echium portosanctense, Fumaria muralis subsp. muralis var. laeta, Helichrysum melaleucum subsp. roseum, Lotus glaucus subsp. floridus, Lotus loweanus, Monizia edulis subsp. santosii, Sonchus parathalassius, Limonium lowei, Pericallis menezesii, Saxifraga portosanctana, Erysimum arbuscula, Vicia costae, Vicia ferreirensis and Sideritis candicans var. multiflora), 28 are endemic to Madeira and 26 endemic to Macaronesia, among the approximately 536 identified taxa.

Part of this flora is of ancient origin (paleoendemic flora), showing traces of Tertiary vegetation that predominated in the basin of the Archaic ocean Tethys, where the Mediterranean sea is now located, while another part presents a more recent evolutionary tendency (non-endemic flora), where the arborescent caulirosulate or candelabra like or woody monocarpic plant aspect are evidence of an insular evolutionary tendency called Island woodiness. Several endemisms are listed in Annex II of the Habitats Directives such as: Chamaemeles coriacea, Cheirolophus massonianus, Maytenus umbellata, Monizia edulis, Phagnalon lowei (P. benettii), Semele androgyna (S. maderensis), Autonoe madeirensis (Scilla maderensis) and Sibthorpia peregrina.

Associated to the vascular flora is an interesting diversity of nonvascular plants, the bryophytes, with 133 identified taxa, of which seven are endemic, two being endemic to Madeira (Riccia atlantica and Frullania sergiae) and five to Macaronesia (Fissidens coacervatus, Leucodon treleasei, Tortella limbata, Frullania polysticta and Radula wichurae).

In relation to lichens, although their presence is abundant and stands out in the landscape due to the yellowish, orange and off-white shades they confer onto the rocky outcrops, only 16 species have been cited, with Anzia centrifuga endemic to Porto Santo.

In marine flora, the algae that are most noteworthy are the green algae, from the Enteromorpha genus and the species Dasycladus vermicularis and Penicillus capitatus. Among the brown algae, there are Padina pavonica and Cystoseira sp.