Reading in a second language (L2) is a complex task that entails an interaction between L2 and the native language (L1). Previous studies have suggested that bilingual subjects recruit the neural system of their logographic L1 (Chinese) reading and apply it to alphabetic L2 (English) reading. These findings have lent strong support to the idea that language experience shapes the cortex. Whether languages of the same writing system such as Japanese Kanji and Chinese characters, would also utilize the same neural substrates is still unclear. In this study, we used functional magnetic resonance imaging (fMRI) to visualize Japanese-Chinese bilinguals' brain activity in phonological processing of Japanese Kanji (L1) and Chinese characters (L2), two written languages with highly similar orthography. In the experiment, the subjects were asked to judge whether two Japanese Kanji (or Chinese characters) presented at the left and right side of the fixation point rhymed with each other. A font size decision task was used as a control task, where the subjects judged whether the two Japanese Kanji (or Chinese characters) had an identical physical size. Subjects indicated a positive response by pressing the key corresponding to the index finger and a negative response by pressing the key corresponding to the middle finger of their right hand. The result showed that our bilingual Japanese subjects have large overlaps in the neural substrates for phonological processing of both native and second language. Our finding supports the idea that the neural systems of second language reading are shaped by native language.