The present study, from a cross-linguistic perspective, investigated to what extent the native word and/or intonation prosody influence the lexical encoding of L2 Mandarin tones. Advanced Seoul Korean (SK) learners of Mandarin and advanced Russian learners of Mandarin were selected as participants in that SK and Russian differ in word prosodic system. Russian uses word stress while SK employs no word prosodic cues. A lexical decision task was applied where participants were required to judge whether the disyllabic words/nonwords they heard were real words. It was found that overall the advanced SK learners and the advanced Russian learners performed significantly worse than the natives, showing that their lexical encoding of Mandarin tones was not native-like. The advanced SK learners (with a rich inventory of pitch accents in the native intonation) significantly outperformed the advanced Russian learners (with comparably fewer intonational pitch accents) , suggesting that the native intonation prosody may better play a role in encoding Mandarin tones lexically than word prosody for non-tonal L2 learners. Furthermore, language-specific and language-general patterns were found in the lexical encoding of L2 Mandarin tonal contrasts, which were discussed in terms of perceptual models and the influence of the native prosody systems.