Creating a list of pairs after splitting the string containing all of the sets
You could create your own custom section in your config file.

First define what each record looks like:

public class Department : ConfigurationSection
{
    [ConfigurationProperty("name", IsRequired = true)]
    public string Name
    {
        get { return (string)this["name"]; }
        set { this["name"] = value; }
    }

    [ConfigurationProperty("assignee", IsRequired = true)]
    public string Assignee
    {
        get { return (string)this["assignee"]; }
        set { this["assignee"] = value; }
    }
}


Define the a collection so the framework can work with your section

public class DepartmentCollection : ConfigurationElementCollection
{
    public override ConfigurationElementCollectionType CollectionType
    {
        get { return ConfigurationElementCollectionType.BasicMap; }
    }

    protected override string ElementName
    {
        get { return "Department"; }
    }

    protected override ConfigurationPropertyCollection Properties
    {
        get { return new ConfigurationPropertyCollection(); }
    }

    public Department this[int index]
    {
        get { return (Department) BaseGet(index); }
        set
        {
            if (BaseGet(index) != null)
            {
                BaseRemoveAt(index);
            }
            base.BaseAdd(index, value);
        }
    }

    public Department this[string name]
    {
        get { return (Department) BaseGet(name); }
    }

    public void Add(Department item)
    {
        base.BaseAdd(item);
    }

    public void Remove(Department item)
    {
        BaseRemove(item);
    }

    public void RemoveAt(int index)
    {
        BaseRemoveAt(index);
    }

    protected override ConfigurationElement CreateNewElement()
    {
        return new Department();
    }

    protected override object GetElementKey(ConfigurationElement element)
    {
        return (element as Department).Name;
    }
}


Define what the list looks like

public class DepartmentList : ConfigurationSection
{
    private static readonly ConfigurationPropertyCollection DepartmentListProperties;
    private static readonly ConfigurationProperty DepartmentProperty;

    static DepartmentList()
    {
        DepartmentProperty = new ConfigurationProperty(
            "",
            typeof (DepartmentCollection),
            null,
            ConfigurationPropertyOptions.IsRequired | ConfigurationPropertyOptions.IsDefaultCollection
            );

        DepartmentListProperties = new ConfigurationPropertyCollection
                                       {
                                           DepartmentProperty
                                       };
    }

    public DepartmentCollection Departments
    {
        get { return (DepartmentCollection) base[DepartmentProperty]; }
        set { base[DepartmentProperty] = value; }
    }

    protected override ConfigurationPropertyCollection Properties
    {
        get { return DepartmentListProperties; }
    }
}


Now, in your .config file specify the new type:

&lt;configSections&gt;
    &lt;section name="DepartmentAssigneeMapping" type="DatabaseCleanup.DepartmentList, DatabaseCleanup, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null"/&gt;
&lt;/configSections&gt;


and add your section

&lt;DepartmentAssigneeMapping&gt;
    &lt;Department name="Depart1" assignee="PersonAssignTo1" /&gt;
    &lt;Department name="Depart2" assignee="PersonAssignTo2" /&gt;
&lt;/DepartmentAssigneeMapping&gt;


Now, in your class:

public List&lt;string&gt; departmentList;
public List&lt;string&gt; assignedtoList;

var mappings = (DepartmentList) ConfigurationManager.GetSection("DepartmentAssigneeMapping");

departmentList = (
    from Department department in mappings.Departments 
    select department.Name).ToList();
assignedtoList = (
    from Department department in mappings.Departments 
    select department.Assignee).ToList();


Your class is much nicer, and the config is way cleaner.

This is fully tested, and the results you are looking for are replicated.