I assume from your description that one of the clients is written in Java (JMS) and the other one is written in an other language and both have access to the same queue. MQ-Series is a queuing product, JMS is a Java API (like JDBC is to relational databases). MQ-Series supports the JMS API so there is no problem in communciating messages. JMS will probably be a subset of possible MQ-Series features.
Make sure that the content can be interpreted by both parties. The standard way is to use XML in the message. But you could use any other format that both clients can understand. You could also use CSV (comma separated values), JSON (JavaScript object notation) and there are even cross platform binary formats like Hessian.
But if you could be more specific about the participants and the kind of information you want to communicate, you probably would get more specific answers.