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Refer

http://en.wikipedia.org/wiki/Comparison_of_C_Sharp_and_Java

1. All methods are virtual by default in java and non-virtual in c#
2. C# has concept of partial classes, java does not.
3. In C#, you can have multiple public classes in a source file while in Java you can only have one public class per file. In java file name must match the public class name, this is not a requirement in C#.
4. C# has limited support for pointers, java does not.
5. Java uses JVM, C# uses CLR. Java code can run on multiple OS while C# code runs on Windows OS only.

there are many more...

in addition to tejas's point 5, C# code can run on linux, mac os, playstation, xbox, iOS and android.