Square Enix appears to have another game in its Mana series in development, judging by the title given on a Japanese compilation soundtrack. A Christmas album titled The X'mas Collections II features holiday versions of familiar songs from series like Final Fantasy and SaGa Frontier, but one track may have revealed unannounced plans.
The ninth song on the album (via CVG) notes that the track is from "Seiken Densetsu (Future Project)." That's the Japanese name for the Mana series in the West, consisting of games like Secret of Mana. It was also composed by Yoko Shimomura, who wrote the score for both Legend of Mana and Heroes of Mana.
That said, Square Enix most recently released the mobile game Circle of Mana. It's entirely possible that whatever this future Mana game might be, it won't be a traditional console release like most of its predecessors.