MP4 and MKV

MP4 is a video format that developed by the Moving Picture Experts Group (MPEG); commonly used for sharing video files on the Internet. The MPEG-4 video is compressed with MPEG-4 video encoding. Audio is compressed using AAC compression.

MKV is an open standard free container format, a file format that can hold an unlimited number of video, audio, picture or subtitle tracks inside a single file. It is mostly used to store compressed movie files, due to the large file size of bluray movies, most users have chosen to compress them into mkv's, when using a good codec (x.264, h.264, etc) you get good quality with smaller sizes, a 25gig bluray movie can be compressed to about 7-8gigs with very little loss in resolution

Summary:
1: MP4 is more compatibility, MKV with better quality
2: MP4 is another compression format/container typically used to get movies into a format for portable players (such as iPad/iPod/iPhone).
3: MKV is mostly used to store compressed movie files, when using a good codec (h.264, etc) you get good quality with smaller sizes.
4: The advantage of MKV is that everything is separated so if you add your subs the will not be hard coded (burned in) on the video so you can toggle them on or off

Other Comparison: MOV vs WMV / 3GP vs 3G2 / MP4 vs FLV / MKV vs MP4 / MP4 vs MP3 / 3GP vs MOV / 3GP vs FLV / M2TS vs MP4

Related Post of MP4 File formats

Related Post of MKV File formats