Nepenthes micramphora was formally described in 2009 by Volker Heinrich, Stewart McPherson, Thomas Gronemeyer, and Victor Amoroso. The description was published in the second volume of McPherson's Pitcher Plants of the Old World. The herbarium specimen V.Amoroso & R.Aspiras CMUH 00003545 is the designated holotype, and is deposited at the Central Mindanao University Herbarium in Musuan, Bukidnon, the Philippines. It was collected on 31 January 2005, from Mount Hamiguitan, on the trail from San Isidro, at an altitude of 1300-1600 m.