The flowers with a cream white to yellowish ground colour are fleshy and do not open widely.

Despite the colouration, it has not been widely used in hybridisation, as the flowers are strongly cupped and have other underireable traits, which are expressed in offspring.

White forms of this species are categorized as Phalaenopsis javanica f. alba O.Gruss & Roellke ex Christenson.

After the publication of Phalaenopsis floresensis taxonomic confusion arose, due to the misleading photographs, which were taken of not yet fully open flowers.

This mistake was reinforced by second appearance in print, in which Phalaenopsis floresensis again were photographed in a premature stage.