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I understand that Linux uses shebang line to determine what interpreter to use for scripting languages, but how does it work for binaries?

I mean I can run Linux binaries, and having installed both wine and mono, Windows native and .NET binaries. And for all of them it's just ./binary-name (if not in PATH) to run it.

How does Linux determine that a given binary must be run as a Linux native binary, as a Windows native binary (using wine facilities) or as a Windows .NET binary (using mono facilities)?

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In a word: binfmt_misc. It's a Linux-specific, non-portable, facility.

There are a couple of formats that are recognized by the kernel with built-in logic. Namely, these are the ELF format (for normal binaries) and the shebang convention (for scripts). (thanks to zwol for the following part of the answer). In addition, Linux recognizes a couple of esoteric or obsolete or compatibility builtin formats. You probably won't encounter them. They are a.out, "em86", "flat", and "elf_fdpic".

Everything else must be registered through the binfmt_misc system. This system allows you to register with the kernel a simple pattern check based on a magic number, and the corresponding interpreter.

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    Although the OP asked for Linux explicitly, it could be worth noting that unlike many other solutions that work both on Linux and other Unix-like systems, this one is totally Linux-specific. – cubuspl42 Apr 26 '15 at 18:57
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    It might not be compiled in, but the Linux source tree still includes intrinsic support for a.out, "em86", "flat", and "elf_fdpic" formats as well as normal ELF. All of those except em86 appear to be native binary executable formats; there isn't enough information for me to figure out when one would use "flat" or "elf_fdpic". em86 appears to be a pre-binfmt_misc mechanism for running a particular x86 emulator, it's probably only still around for backward compatibility. – zwol Apr 26 '15 at 22:14
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    On Debian Linux (I didn't check RedHat and others) the command to display all current binfmt entries is update-binfmts --display – golem Apr 27 '15 at 16:29

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