If you have persistence.xml file in your project and you're using ORM framework like hibernate or toplink
<property name="toplink.jdbc.url" value="jdbc:mysql://localhost:3306/SCHEMA_NAME?characterEncoding=UTF-8" />

Otherwise in your code when you want to create a connection (JDBC) you have change your URL address.
I think using ?characterEncoding=UTF-8 will solve your problem