MaK11-12 has released a new version of Ctrmus a music player for the 3DS. It plays PCM WAV, AIFF, FLAC, OPUS and MP3. Music continues to play when the 3DS is closed.

Heres whats new:

Updated 2016-01-05 (0.4.4):

Add directory browsing. Directories are coloured blue.
Add MP3 file support.

More info --> https://github.com/deltabeard/ctrmus

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