Update - 2014-04-16

As pointed out in the comments below - mkvmerge --split now has a chapters option

  mkvmerge -o output.mkv --split chapters:1,3,5 testfile.mkv

I have no idea how long that option has been there - but it certainly makes life a lot easier. Thanks to the commmenter for the update.

Original post

The original post shows how to do timecode based splitting which may still be useful for people:

I had the need to split some mkv (matroska video) files on chapter marks.

I'd normally use handbrake for this - split and encode. But I didn't really want to reencode each time.

Downloaded mkvtoolsnix (machomebrew: brew install mkvtoolsnix).

Most tutorials concentrate on mkvmerge gui which I didn't have - just the command line

So - an example:

    $ mkvinfo testfile.mkv  | grep ChapterTimeStart
        |   + ChapterTimeStart: 00:00:00.000000000
        |   + ChapterTimeStart: 00:08:45.000000000
        |   + ChapterTimeStart: 00:14:47.856000000
        |   + ChapterTimeStart: 00:19:03.576000000
        |   + ChapterTimeStart: 00:27:23.656000000
        |   + ChapterTimeStart: 00:36:08.496000000
        |   + ChapterTimeStart: 00:41:30.776000000
        |   + ChapterTimeStart: 00:45:42.896000000
        |   + ChapterTimeStart: 00:51:40.256000000
        |   + ChapterTimeStart: 01:03:57.336000000
        |   + ChapterTimeStart: 01:16:19.296000000
        |   + ChapterTimeStart: 01:26:53.456000000

Let's say we want to split off the first chapter:

$ mkvmerge -o output.mkv --split "timecodes:00:08:45.00" testfile.mkv

timecodes has hh:mm:ss.ss (hours, mins, secs in decimal) as format and can take comma sep list for splitting at several points.

Bingo - chapter split matroska video still in matroska with all video and subtitles intact and no reencoding.