Nepenthes hamiguitanensis was initially assumed to represent a natural hybrid between N. micramphora and N. peltata, both of which are also present on the upper slopes of Mount Hamiguitan. It shares several morphological features with its putative parent species, such as the shape of the pitchers (with N. micramphora) and form of the indumentum (with N. peltata). However, it has distinctive light-coloured upper pitchers that neither of these species possess (N. peltata is not known to produce aerial traps at all). In addition, N. hamiguitanensis inhabits a different ecological niche to either of these species; it typically grows in partial shade under the cover of mountain forest or at forest margins, whereas N. micramphora and N. peltata are commonly found in more exposed sites.