In many to mant relationship each row in table A linked to multiple rows in table B and vice versa.Here is an example of Student and course. one student can chose multiple subject in the same way 1 course can be assigned to multiple student.

Configuration file : hibernate.cfg.xml

<?xml version='1.0' encoding='utf-8'?>
<!DOCTYPE hibernate-configuration PUBLIC
"-//Hibernate/Hibernate Configuration DTD//EN"
"http://hibernate.sourceforge.net/hibernate-configuration-3.0.dtd">

<hibernate-configuration>
    <session-factory>
        <property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
        <property name="hibernate.connection.url">jdbc:mysql://localhost:3306/hibernaterelationship</property>
        <property name="hibernate.connection.username">root</property>
        <property name="hibernate.connection.password">root</property>
        <property name="hibernate.connection.pool_size">10</property>
        <property name="show_sql">true</property>
        <property name="dialect">org.hibernate.dialect.MySQLDialect</property>
        <property name="hibernate.hbm2ddl.auto">create-drop</property>

        <!-- Mapping files -->
        <mapping class="net.roseindia.table.Course" />
        <mapping class="net.roseindia.table.Student" />

    </session-factory>
</hibernate-configuration>

Table classes :

Course.java

package net.roseindia.table;

import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.Id;
import javax.persistence.Table;

@Entity
@Table(name = "course")
public class Course {

    private int courseId;
    private String courseName;

    public Course(String course) {
        // TODO Auto-generated constructor stub
        this.courseName=course;
    }

    @Id
    @GeneratedValue
    @Column(name = "courseId", nullable = false)
    public int getCourseId() {
        return courseId;
    }

    public void setCourseId(int courseId) {
        this.courseId = courseId;
    }

    @Column(name = "courseName", nullable = false)
    public String getCourseName() {
        return courseName;
    }

    public void setCourseName(String courseName) {
        this.courseName = courseName;
    }

}

Student.java

package net.roseindia.table;

import java.util.HashSet;
import java.util.Set;

import javax.persistence.CascadeType;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.Id;
import javax.persistence.ManyToMany;
import javax.persistence.Table;

@Entity
@Table(name="student")
public class Student {
    private int id;
    private String name;
    private Set<Course> courses = new HashSet<Course>();

    public Student(String name) {
        // TODO Auto-generated constructor stub
        this.name = name;
    }

    public Student(String name, Set<Course> courses) {
        this.name = name;
        this.courses = courses;
    }

    @Id
    @GeneratedValue
    @Column(name = "studentId", nullable = false)
    public int getId() {
        return id;
    }

    public void setId(int id) {
        this.id = id;
    }

    @Column(name = "studentName", nullable = false)
    public String getName() {
        return name;
    }

    public void setName(String name) {
        this.name = name;
    }

    @ManyToMany(cascade=CascadeType.ALL)
    public Set<Course> getCourses() {
        return courses;
    }

    public void setCourses(Set<Course> courses) {
        this.courses = courses;
    }



}

Continued..

Util Class:HibernateUtil.java

package net.roseindia.util;

import org.hibernate.SessionFactory;
import org.hibernate.cfg.AnnotationConfiguration;

public class HibernateUtil {
    private static SessionFactory sessionFactory = null;

    static {
        sessionFactory = new AnnotationConfiguration().configure()
                .buildSessionFactory();
    }

    public static SessionFactory getseSessionFactory() {
        return sessionFactory;
    }
}

Main Class : ManyToMany.java

package net.roseindia.application;

import java.util.HashSet;
import java.util.Set;

import net.roseindia.table.Course;
import net.roseindia.table.Student;
import net.roseindia.util.HibernateUtil;

import org.hibernate.HibernateException;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.hibernate.Transaction;

public class ManyToMany{
    public static void main(String[] args){
        Session session=HibernateUtil.getseSessionFactory().openSession();
        Transaction transaction=null;
        try{
            transaction=session.beginTransaction();
            Set<Course> courses=new HashSet<Course>();
            courses.add(new Course("Maths"));
            courses.add(new Course("Science"));

            Student student1=new Student("Ron", courses);
            Student student2=new Student("Ric",courses);
            session.save(student1);
            session.save(student2);
            transaction.commit();

        }catch(HibernateException he){
            System.out.println(he.getMessage());
        }
        finally{
            session.close();
        }
    }
}

Output:

Hibernate: insert into student (studentName) values (?)
Hibernate: insert into course (courseName) values (?)
Hibernate: insert into course (courseName) values (?)
Hibernate: insert into student (studentName) values (?)
Hibernate: insert into student_course (student_studentId, courses_courseId) values (?, ?)
Hibernate: insert into student_course (student_studentId, courses_courseId) values (?, ?)
Hibernate: insert into student_course (student_studentId, courses_courseId) values (?, ?)
Hibernate: insert into student_course (student_studentId, courses_courseId) values (?, ?)

see this simple annotation example