Nepenthes micramphora is very similar to N. bellii of northern Mindanao in terms of the morphology of its stem, lamina, and inflorescence. Indeed, prior to the description of N. micramphora in 2009, the species was misidentified as N. bellii on its native Mount Hamiguitan. Nepenthes micramphora is smaller in all respects and can be distinguished on the basis of its pitchers, which differ markedly in shape, size, peristome width, and tendril length. It also produces a greater abundance of pitchers on its rosettes — up to 7 live traps have been recorded at any one time.