The flowers have a rounded but slightly triangular ovary; their segments are wide opened with yellow green sepals and petals, transversally stained or striped of brown; and white labellum with a yellow warted callus close to the base surrounded by brown orange stains.
Although closely related to Miltonia, Phymatochilum brasiliense does not have many morphologic characteristics in common with them: It presents much more robust pseudobulbs and leaves, which also are of different color and shapes.