JAXB (JSR-222) does not offer a standard way to specify the namespace prefix used.
Extension - NamespacePrefixMapper
For the JAXB reference implementations and recent versions of EclipseLink JAXB (MOXy) you can use the NamespacePrefixMapper extension to control the namespace prefixes used.
MyNamespaceMapper
import com.sun.xml.internal.bind.marshaller.NamespacePrefixMapper;
//import com.sun.xml.bind.marshaller.NamespacePrefixMapper;
public class MyNamespaceMapper extends NamespacePrefixMapper {
    private static final String FOO_PREFIX = ""; // DEFAULT NAMESPACE
    private static final String FOO_URI = "http://www.example.com/FOO";
    private static final String BAR_PREFIX = "bar";
    private static final String BAR_URI = "http://www.example.com/BAR";
    @Override
    public String getPreferredPrefix(String namespaceUri, String suggestion, boolean requirePrefix) {
        if(FOO_URI.equals(namespaceUri)) {
            return FOO_PREFIX;
        } else if(BAR_URI.equals(namespaceUri)) {
            return BAR_PREFIX;
        }
        return suggestion;
    }
    @Override
    public String[] getPreDeclaredNamespaceUris() {
        return new String[] { FOO_URI, BAR_URI };
    }
}
Specifying the NamespacePrefixMapper
Below is an example of how the NamespacePrefixMapper is set on the Marshaller.
    Marshaller m = ctx.createMarshaller();
    m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
    try {
        m.setProperty("com.sun.xml.internal.bind.namespacePrefixMapper", new MyNamespaceMapper());
        //m.setProperty("com.sun.xml.bind.namespacePrefixMapper", new MyNamespaceMapper());
    } catch(PropertyException e) {
        // In case another JAXB implementation is used
    }
Extension - Leveraging @XmlSchema
EclipseLink JAXB (MOXy) and recent versions of the JAXB reference implementation will use the namespace prefixes defined on the package level @XmlSchema annotation.
@XmlSchema(
    elementFormDefault=XmlNsForm.QUALIFIED,
    namespace="http://www.example.com/FOO",
    xmlns={
        @XmlNs(prefix="", namespaceURI="http://www.example.com/FOO")
        @XmlNs(prefix="bar", namespaceURI="http://www.example.com/BAR")
    }
)
package blog.prefix;
import javax.xml.bind.annotation.*;
For More Information