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From java, you can call .dll / .so either using JNI (the standard way, but more tedious, but you have to write wrappers yourself) or using JNA. The easiest way is to use JNA (but it's slower).
From C#, as far as I understand, you can call any dll using dllimport or something like that, but, in any case, this is not a very wise decision to combine code in one language and dll in another, there will be a bunch of unhandled errors that occur sporadically, which are quite difficult to track.
Java does not allow you to create dlls, so "the other way around" is not possible. If the method described by lair does not suit you, then you can use sockets for communication between processes or threads (depending on how you load the modules).
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