Custom Settings :
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You can deploy the custom setting definition between orgs,but the data must be transferred separately.
Records can be created,modified and deleted using Apex DML.
Preferred for managed packages and scenarios with custom configuration UI in visualForce or Lightning.
Custom Metadata :
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You can deploy the custom metadata types and the custom metadata records between orgs.
Records can be created,modified and deleted from the UI or metadata API-but not through Apex.
Preferred for development in specific organizations where custom configuration UI is not required.
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