interface IEntity { }
interface IDto { }

class Parent : IEntity
{
    public IList<Child> Childs { get; set; }
}
class Child : IEntity
{
    IEntity Parent { get; set; }
}
////////////////DTOs////////////////
class ChildDto : IDto
{
    IDto Parent { get; set; }
}
class ParentDto : IDto
{
    public IList<ChildDto> Childs { get; set; }
}

public void Test()
{
    Mapper.CreateMap<Child, ChildDto>();
    Mapper.CreateMap<ChildDto, Child>();
    Mapper.CreateMap<Parent, ParentDto>();
    Mapper.CreateMap<ParentDto, Parent>();

    var parent = new Parent();
    var child = new Child { Parent = parent };
    parent.Childs.Add(child);

    var parentDto = Mapper.Map<ParentDto>(parent);
}

Mapper.CreateMap<Child, ChildDto>()
    .MapFrom(x => x.Parent, o => o.ResolveUsing(x =>
{
    var sourceType = x.Parent.GetType();
    var destType = (from maps in Mapper.GetAllTypeMaps()
                    where maps.SourceType == sourceType
                    select maps).FirstOrDefault().DestinationType;
    return Mapper.Map(x.Parent, destType);
}));

    Mapper.CreateMap<Child, ChildDto>();
    Mapper.CreateMap<ChildDto, Child>();
    Mapper.CreateMap<Parent, ParentDto>();
    Mapper.CreateMap<ParentDto, Parent>();
    // Пока сделал так
    Mapper.CreateMap<Parent, IDto>().As<ParentDto>();