Marketo has the ability to merge a SFDC Lead with a Contact record if the Marketo user has the “Merge Leads” permission and the Marketo user profile in SFDC has the ability to covert leads, create contacts, accounts and opportunities.
If a Lead and Contact are merged in Marketo, the Lead will first be converted into a Contact, then merged with the other Contact.
The Contact is the primary record.
I do not recommend allowing the Marketo profile to convert SFDC leads to contacts. Marketo will automatically create a new account and opportunity. Marketo cannot convert the Lead into an existing Account, because it would not know which Account to associate the converted record.
When you merge records in Marketo, in the case of conflicts you can choose which value to keep. If you don't want either value, you can check Custom and enter a value of your choice. Thus, you get to choose which scoring values you want or you can enter a new value.
After the Merge
The default Lead Score field and all other custom score fields are not added up since you chose the score to keep during the merge. The complete activity logs will be merged in Marketo including membership in all programs. Last Interesting Moments will be merged in Sales Insight.
Here is a detailed article by Grant Booth on understanding merges in Marketo.
Here is more information about using the Convert Lead flow step.
When to Use Marketo to Merge Records
I recommend only using Marketo to merge records if one of the records is in Marketo only. If two or more records are in SFDC, you should use SFDC to merge the records since all the SFDC fields might not be synced to Marketo and you won't be able to address those field conflicts.
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