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You can only have one identity source per organization in an AWS Organization. Refer Manage your identity source documentation and FAQ question Can I connect more than one identity source to IAM Identity Center.
On your second question, why ListInstances returns array of instances, I'd suggest you to look at FAQ question How do I start using IAM Identity Center, point #2 says following:
You can also change directory to connect to a Microsoft AD directory by clicking through a list of Managed Microsoft AD and AD Connector instances that IAM Identity Center discovers in your account automatically.
There can be multiple AD Connector instances that IAM Identity Center discovers in your account automatically and caller who has access to this IAM Identity Center, may get list of all those instances.
Hope it helps.
Abhishek
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Maybe using the ListInstnaces API is not what I want to use.. What i want to find is the IdentityStoreId.. Will this be the same for all instsances perhaps?
I could'nt find a better API to call. I really need to do this programatically..
Yes, that's right, identity store id would be same as there would be one identity store only. Unfortunately there is no API or CLI command available to fetch the identity store id programmatically. Hope that answers your question. Completely optional, if this answers your question, you can approve the answer.