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I'm not familiar with Dynamics, but I can speak towards SF and I'd anticipate it to be similar in this case. Quick to the point, when you connect your CRM, every lead will sync into Marketo. Thus creating duplicates. There is no matching done on Marketo's side.
This is due to unique ID's associated to the records. You will have to do a data merge project with either Marketo or a vendor.
This is how my SF integration went and I was in the exact same situation.
This is correct for SFDC - Marketo trusts SFDC and doesn't dedupe leads coming from SFDC.
I always recommend you clean your CRM before integrating. If you happen to have an existing Marketo, try RingLead to help merge between systems.