The two statements that best describe similarities between the Middle Colonies and the New England Colonies are:
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Both had mostly good relationships with Native Americans, even though there were some conflicts. - While there were conflicts, both regions initially engaged in trade and formed various agreements with Native American tribes.
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Both had some groups that settled for religious reasons. - Both regions included groups that sought religious freedom, such as the Pilgrims and Puritans in New England and various religious groups (like Quakers) in the Middle Colonies.