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It really depends on which application you have...the algorithms for speech recognition are different from speech indentification for example. Based on what you need, just look for an open source library for Java. Getting into the theory is definitely desired but as a first step you can just look for a software block that has inputs/outputs, later you can drill into it.  

Here is some info on speech recog: https://stackoverflow.com/questions/3018418/open-source-simple-speech-recognition-in-c-in-windows