Applying IPSec to Domain Controllers

The problem you have provided a link to only applies to Windows 2000.
How would you like to secure the Domain Controllers? All comms to and from the server?
The simplest way for you would be to use the pre-set 'Secure Server (Require Security)' policy. This will demand that all clients have to use the 'Client (Respond Only)' policy. This setup will make the two machines negotiate the most secure mutually agreeable level of security.
Using these two pre-set policies will keep thing simple. As long as your clients are configured properly, then you will be able to RDP into the DC while it is secured with IPSEC.

I have configured the IPSec through GPO and linked it to the Domain Controllers OU.
If I try to create another IPsec policy for servers OU, it won't let me assign both IPSec policies, it will assign just one.
SO how do I create 2 IPSec policies , one to Domain Controllers OU and one to Servers OU?

I see no reason why you shouldn't be able to assign to IPSEC policies to separate OUs.

Are either of these OUs child/parent of each other? Where exactly did you link your GPO? Directly to the OUs in question?

I have previously applied different IPSEC policies to separate OUs with no conflicts.

if you create a GPO for another OU and go to computer configuration/ security settings/ IPSec....
on the right pane the IPsec policy you set up reviously will showup there, even though you are setting up a GPO to a  completeky different OU.

bluntTony:I see no reason why you shouldn't be able to assign to IPSEC policies to separate OUs.

did you try it?

Yes, I have tested this. I applied the 'Secure Server' policy to the Domain Controllers OU, and the 'Client' policy to a separate OU holding some computer accounts.

It is true that you can only have one IPSEC policy at the same level (i.e. policies will not merge, one will overrule the other), but as long as one OU isn't inheriting both GPOs you should be able to do this.

I don't know how you did it. But even if I go to another OU /Right click /properties/Group policy and select new then create a new policy /edit /windows settings/security settings /IP Security Policies on Active Directory(Mydomainame.com)
on the right pane I will still see the previous policy I have created for the Different OU.

Have you set up your own IPSEC policy? Are you saying that when you create a new GPO, the policy is listed AND it is ticked green (i.e. it's assigned)?

If it's just listed, it doesn't mean it's been assigned. You have to select the policy, and select 'Assign' for it to apply.

I will take a llok at it later when I remote to the Network.

As of RDP I fixed it. I was unable to RDP to my DC because it's  a little bit tricky the IP filter List/Protocl.
I should have type 3389 in the From this port field To any port. Indtead I select from any port to this port 3389.
so I just swapped the settings and managed to RDP.
But the File Replication is not working either. For instance if you create a file under logon share in one DC it does not replicate to the Netlogon share in the other DC. I opened port TCP/UDP135 and TCP random port 50000 but still didn't work. I am not sure if I need to tweak a registery to make it know about the port 50000.

sorry fir the typos