Phonemes play a central role in traditional theories as units of speech perception and access codes to lexical representations. Phonemes have two essential properties: they are ‘segment-sized’ (the size of a consonant or vowel) and abstract (a single phoneme may be have different acoustic realisations). Nevertheless, there is a long history of challenging the phoneme hypothesis, with some theorists arguing for differently sized phonological units (e.g. features or syllables) and others rejecting abstract codes in favour of representations that encode detailed acoustic properties of the stimulus. The phoneme hypothesis is the minority view today. We defend the phoneme hypothesis in two complementary ways. First, we show that rejection of phonemes is based on a flawed interpretation of empirical findings. For example, it is commonly argued that the failure to find acoustic invariances for phonemes rules out phonemes. However, the lack of invariance is only a problem on the assumption that speech perception is a bottom-up process. If learned sublexical codes are modified by top-down constraints (which they are), then this argument loses all force. Second, we provide strong positive evidence for phonemes on the basis of linguistic data. Almost all findings that are taken (incorrectly) as evidence against phonemes are based on psycholinguistic studies of single words. However, phonemes were first introduced in linguistics, and the best evidence for phonemes comes from linguistic analyses of complex word forms and sentences. In short, the rejection of phonemes is based on a false analysis and a too-narrow consideration of the relevant data.