We examined the role of different cognitive skills in word reading (accuracy and fluency) and spelling accuracy in syllabic Hiragana and morphographic Kanji. Japanese Hiragana and Kanji are strikingly contrastive orthographies: Hiragana has consistent character-sound correspondences with a limited symbol set, whereas Kanji has inconsistent character-sound correspondences with a large symbol set. One hundred sixty-nine Japanese children were assessed at the beginning of grade 1 on reading accuracy and fluency, spelling, phonological awareness, phonological memory, rapid automatized naming (RAN), orthographic knowledge, and morphological awareness, and on reading and spelling at the middle of grade 1. The results showed remarkable differences in the cognitive predictors of early reading accuracy and spelling development in Hiragana and Kanji, and somewhat lesser differences in the predictors of fluency development. Phonological awareness was a unique predictor of Hiragana reading accuracy and spelling, but its impact was relatively weak and transient. This finding is in line with those reported in consistent orthographies with contained symbol sets such as Finnish and Greek. In contrast, RAN and morphological awareness were more important predictors of Kanji than of Hiragana, and the patterns of relationships for Kanji were similar to those found in inconsistent orthographies with extensive symbol sets such as Chinese. The findings suggested that Japanese children learning two contrastive orthographic systems develop partially separate cognitive bases rather than a single basis for literacy acquisition.