Danser considered N. tomoriana from Sulawesi and N. distillatoria from Sri Lanka to be the closest relatives of N. neoguineensis.
He also noted its similarity to N. papuana, stating: "N. papuana is so much alike N. neoguineensis in its vegetative parts, that only the complete knowledge of the generative parts has suggested me to establish a new species".

The two taxa can be distinguished on the basis of several morphological features.
N. papuana has a racemose inflorescence, while that of N. neoguineensis is a panicle or panicle-like raceme.
Furthermore, the inflorescence of N. papuana usually bears only one-flowered pedicels, both in male and female plants.
Those of N. neoguineensis can be up to four-flowered.

The lamina of N. papuana has very distinct longitudinal veins and indistinct pinnate veins, whereas in N. neoguineensis the opposite is true.
In addition, the leaves of N. papuana are very densely ciliate, much more so than in N. neoguineensis.
The wings are less developed in the upper pitchers of N. papuana and the fringe elements are more closely spaced.

Based on the structure of its inflorescence, it has been suggested that N. neoguineensis belongs to a group of relatively primitive Nepenthes species, which includes N. distillatoria and N. pervillei.
Danser considered N. tomoriana from Sulawesi and N. distillatoria from Sri Lanka to be the closest relatives of N. neoguineensis. He also noted its similarity to N. papuana, stating: "N. papuana is so much alike N. neoguineensis in its vegetative parts, that only the complete knowledge of the generative parts has suggested me to establish a new species".
The two taxa can be distinguished on the basis of several morphological features. N. papuana has a racemose inflorescence, while that of N. neoguineensis is a panicle or panicle-like raceme. Furthermore, the inflorescence of N. papuana usually bears only one-flowered pedicels, both in male and female plants. Those of N. neoguineensis can be up to four-flowered.
The lamina of N. papuana has very distinct longitudinal veins and indistinct pinnate veins, whereas in N. neoguineensis the opposite is true. In addition, the leaves of N. papuana are very densely ciliate, much more so than in N. neoguineensis. The wings are less developed in the upper pitchers of N. papuana and the fringe elements are more closely spaced.
Based on the structure of its inflorescence, it has been suggested that N. neoguineensis belongs to a group of relatively primitive Nepenthes species, which includes N. distillatoria and N. pervillei.
Nepenthes neoguineensis