Flowers appear often within the Metroid series. Similar to trees, many species of flower exist across the various worlds in the games, although most are unnamed and are not part of gameplay.
As an environmental feature
Tallon IV's Tallon Overworld features Red Starbursts, an edible species of red flower that generally blooms in elevator rooms. It appears in Transport to Tallon Overworld West, a room in the Magmoor Caverns. In Super Metroid, the jungle portion of Brinstar features flowers resembling Samus Eaters (see below) that either have long stems or no stems at all, appearing in such rooms as A Bridge Too Far and Hell. Daisies also appear in the Biosphere Test Area surrounding Lyle Smithsonian's body, which causes the scene to resemble a funeral of sorts, especially with the other members of the 07th Platoon surrounding him.
In combat
The Metroid Manga features Badger Glove, a poisonous species of flower that the Space Pirates use to corrupt the Ion-Faeria, necessitating their destruction at the hands of Work Robots, which angers Samus. Later on in the manga, the Space Pirates disguise a Mimic as a bouquet of flowers and use Damara to give it to Chairman Keaton in an attempted assassination, though Samus and Adam manage to destroy it. During Samus' travels on Tallon IV, she comes across Flaahgra, a mutated plant taking up residence inside a large flower that is responsible for the toxicity of the Chozo Ruins water. It is faced as a boss and destroying it cleans the water. Tallon IV also features Bloodflowers, acidic plants that fire dangerous spores at Samus. Flaahgra may have been a Bloodflower.
Blob Throwers, enemies Samus encounters on SR388 resemble flowers with stems, which eject blobs. Samus Eaters are enemies that Samus comes across twice in her adventures: first in Brinstar in Super Metroid, where they resemble red venus flytraps and appear in fungi-infested areas, and in Metroid Fusion, when Samus' battle against the Nettori plant features Samus Eaters (though they resemble Blob Throwers in this appearance and spit blobs), as well as buds that may or may not be unbloomed Eaters.
Finally, one episode of Captain N: The Game Master features "Power Flowers" (which are really normal flowers). Mother Brain deceives Kevin and his friends into believing that the flowers, not Zebetite were the source of fuel for her and Metroid, and this leads them to destroy the flowers so that Kevin can go back home (though he ends up in a replica of his hometown). Mother Brain later states that she has enough power to conquer Videoland "ten times over". Following this, the gang attempts to sabotage shipments of Zebetite to Mother Brain.