Although it is well established that beginning readers rely heavily on phonological decoding, the overlap of the phonological pathways used in visual and auditory word recognition is not clear. Especially in transparent languages, phonological reading could use the same pathways as spoken word processing. In the present study, we report a direct comparison of lexical decision performance in the visual and auditory modality in beginning readers of a transparent language. Using lexical decision, we examine how marker effects of length and frequency differ in the two modalities and how these differences are modulated by reading ability. The results show that both frequency and length effects are stronger in the visual modality, and the differences in length effects between modalities are more pronounced for poorer readers than for better readers. This suggests that visual word recognition in beginning readers of a transparent language initially is based on phonological decoding and subsequent matching in the phonological lexicon, especially for poor readers. However, some orthographic processing seems to be involved already. We claim that the relative contribution of the phonological and orthographic route in beginning readers can be measured by the differences in marker effects between auditory and visual lexical decision.