Nepenthes micramphora has no confirmed natural hybrids, although certain plants from Mount Hamiguitan may represent crosses involving it and N. hamiguitanensis, N. justinae (previously identified as N. mindanaoensis), and N. peltata. Plants that were originally thought to represent a natural hybrid between N. micramphora and N. peltata are now recognised as belonging to a distinct species of possible hybridogenic origin, N. hamiguitanensis.