If two similar sounds do not belong to separate phonemes, they are called allophones of the same underlying phoneme. For instance, voiceless stops (/p/, /t/, /k/) can be aspirated. In English, voiceless stops at the beginning of a stressed syllable (but not after /s/) are aspirated, whereas after /s/ they are not aspirated. This can be seen by putting the fingers right in front of the lips and noticing the difference in breathiness in saying pin versus spin. There is no English word pin that starts with an unaspirated p, therefore in English, aspirated [pʰ] (the [ʰ] means aspirated) and unaspirated [p] are allophones of the same phoneme /p/. This is an example of a complementary distribution.

The /t/ sounds in the words tub, stub, but, butter, and button are all pronounced differently in American English, yet are all intuited to be of "the same sound", therefore they constitute another example of allophones of the same phoneme in English. However, an intuition such as this could be interpreted as a function of post-lexical recognition of the sounds. That is, all are seen as examples of English /t/ once the word itself has been recognized.

The findings and insights of speech perception and articulation research complicates this idea of interchangeable allophones being perceived as the same phoneme, no matter how attractive it might be for linguists who wish to rely on the intuitions of native speakers. First, interchanged allophones of the same phoneme can result in unrecognizable words. Second, actual speech, even at a word level, is highly co-articulated, so it is problematic to think that one can splice words into simple segments without affecting speech perception. In other words, interchanging allophones is a nice idea for intuitive linguistics, but it turns out that this idea can not transcend what co-articulation actually does to spoken sounds. Yet human speech perception is so robust and versatile (happening under various conditions) because, in part, it can deal with such co-articulation.

There are different methods for determining why allophones should fall categorically under a specified phoneme. Counter-intuitively, the principle of phonetic similarity is not always used. This tends to make the phoneme seem abstracted away from the phonetic realities of speech. It should be remembered that, just because allophones can be grouped under phonemes for the purpose of linguistic analysis, this does not necessarily mean that this is an actual process in the way the human brain processes a language. On the other hand, it could be pointed out that some sort of analytic notion of a language beneath the word level is usual if the language is written alphabetically. So one could also speak of a phonology of reading and writing.