MP4s, the latter are significantly smaller in file size, without diminishing the video quality, and tend to be compatible with more media players. MP4s also store information in one file, but looking at MKVs vs. MKV stores subtitle, audio, and video all in one large file and is typically how Blu-rays and DVDs store data for their videos.
Matroska (MKV) and MPEG-4 (MP4) files are both video files capable of storing HD video. A common issue users encounter is to convert MKV files to MP4 files. Different programs use different formats and file extensions, and some will be difficult to playback using some software. Managing video formats and compatibilities can sometimes be a chore.