I am late to the party, but here are the official docs on capturing audio: http://docs.oracle.com/javase/tutorial/sound/capturing.html
(And copied directly from the link above here is some sample code to do it:)
TargetDataLine line;
DataLine.Info info = new DataLine.Info(TargetDataLine.class,
format); // format is an AudioFormat object
if (!AudioSystem.isLineSupported(info)) {
// Handle the error ...
}
// Obtain and open the line.
try {
line = (TargetDataLine) AudioSystem.getLine(info);
line.open(format);
} catch (LineUnavailableException ex) {
// Handle the error ...
}
// Assume that the TargetDataLine, line, has already
// been obtained and opened.
ByteArrayOutputStream out = new ByteArrayOutputStream();
int numBytesRead;
byte[] data = new byte[line.getBufferSize() / 5];
// Begin audio capture.
line.start();
// Here, stopped is a global boolean set by another thread.
while (!stopped) {
// Read the next chunk of data from the TargetDataLine.
numBytesRead = line.read(data, 0, data.length);
// Save this chunk of data.
out.write(data, 0, numBytesRead);
}