String time1 = "16:00:00";
String time2 = "19:00:00";
SimpleDateFormat format = new SimpleDateFormat("HH:mm:ss");
Date date1 = format.parse(time1);
Date date2 = format.parse(time2);
long difference = date2.getTime() - date1.getTime();
Difference is in milliseconds.
I modified sfaizs post.