Since members can belong to one department only. And subdepartments can also belong to one department only - you have one-to-many relationships here.
It's common to store list of keys of these entities. And if needed fetch these entities by their IDs. This approach is commonly used for Big Tables for example in Google Appengine entities.
So I would suggest having 1 entity which stores keys for members and subdepartments.
public class Department {
String name;
String description;
//have to query other Table to get headOfDepartment
Employee headOfDepartment;
//have to query other table to get members
List<Employee_Ids> members;
//have to query other table to get subDepartments.
List<Department_Ids> subDepartments;
}