Background: A large amount of evidence highlights the obvious inequalities in literacy results of South African learners. Despite this, a sound understanding of how learners approach the task of reading in the African languages is lacking. Aim: This article examines the role of the syllable, phoneme and morpheme in reading in transparent, agglutinating languages. The focus is on whether differences in the orthographies of isiXhosa and Setswana influence reading strategies through a comparative study of the interaction between metalinguistic skills and orthography. Setting: Data was collected from Grade 3 first-language and Grade 4 Setswana home language learners attending no fee schools in the Eastern Cape and North West Province respectively. Methods: Learners were tested on four linguistic tasks: an open-ended decomposition task, a phonological awareness task, a morphological awareness task and an oral reading fluency task. These tasks were administered to determine the grain size unit which learners use in connected-text reading. Results: The results indicated that syllables were the dominant grain size in both isiXhosa and Setswana, with the use of morphemes as secondary grains in isiXhosa. These results are reflected in the scores of the metalinguistic tasks. Conclusion: This research contributes to an understanding of how linguistic and orthographic features of African languages need to be taken into consideration in understanding literacy development.