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I am creating a java application which is dependent on a server. On startup the application will transmit sensitive information (passwords and emails) which will be sent to the server and from there encrypted and never be touched again.

My question is how can I secure the client>server transmission from MITM attacks or other attacks that can make the attacker able to read the transmitted data?

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You can use a protocol designed for exactly this: SSL/TLS.

As usual, don't roll your own cryptography. Find an existing implementation that takes care of the heavy lifting for you. For Java, that will probably be the Java Secure Socket Extension (JSSE).

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