This study investigated whether the phonological representation of a word is modulated by its orthographic representation in case of a mismatch between the two representations. Such a mismatch is found in Persian, where short vowels are represented phonemically but not orthographically. Persian adult literates, Persian adult illiterates, and German adult literates were presented with two auditory tasks, an AX-discrimination task and a reversal task. We assumed that if orthographic representations influence phonological representations, Persian literates should perform worse than Persian illiterates or German literates on items with short vowels in these tasks. The results of the discrimination tasks showed that Persian literates and illiterates as well as German literates were approximately equally competent in discriminating short vowels in Persian words and pseudowords. Persian literates did not well discriminate German words containing phonemes that differed only in vowel length. German literates performed relatively poorly in discriminating German homographic words that differed only in vowel length. Persian illiterates were unable to perform the reversal task in Persian. The results of the other two participant groups in the reversal task showed the predicted poorer performance of Persian literates on Persian items containing short vowels compared to items containing long vowels only. German literates did not show this effect in German. Our results suggest two distinct effects of orthography on phonemic representations: whereas the lack of orthographic representations seems to affect phonemic awareness, homography seems to affect the discriminability of phonemic representations.