I need to add a trusted certificate into
The JDK and JRE are different pieces of software, although they are related. Typically the JDK bundle will include the JRE (Java run-time system) plus some other tools. You can use either to run your code, so long as you don't need JDK functionality at runtime (e.g., you're not compiling code on-the-fly). You should put your certificates into whichever (JDK or JRE) you are actually using to run your application.