What is the difference between region file extension .mca and .mcr?

I host a Minecraft 1.8.8 server and I checked my world folder. I went into the DIM and DIM-1 folders and I see .mca files and .mcr files.

What is the difference between these two file extensions?

Solution 1:

.mcr (McRegion) files are part of the older format, where as .mca (Anvil) is a newer format and was introduced in 1.2.1 update to the Java Edition. Main differences are:

• Maximum build height has been increased to 256 (from 128).
• Empty sections of the world are not loaded into memory or saved to disk.
• The maximum Block ID has been increased to 4096 (was 256) by adding a 4-bit data layer (similar to how meta data is stored). The rest of Minecraft's code is not currently prepared to take advantage of this, however.
• Block ordering has been changed from XZY to YZX in order to improve compression.
• Packets for sending chunks have been optimized (a chunk without air is smaller than in the same chunk in the old format, and a chunk with lots of air is even smaller).
• Biomes are saved per X,Z column, rather than being calculated on the fly, which means they can be altered by tools; this is very useful for map makers. It also prevents bugs where features don't match the biome after changing the terrain algorithm. (Also known as "Biome Shifting")

If you see both files, what this means is that your old world files were converted to the new format, but in compatibility mode (hence why old files are left behind). If you wish to save space or reduce backup size, you can delete old .mcr files.