Minutemen and Militia were not strictly the same. They were different because:
The Minutemen formed arguably the first special forces in the colonial armed forces when the American Revolution broke out. They were trained to be able to use weapons and tactics better and were generally handpicked from militias to join the group.
Minutemen were more organized because they were trained to be very mobile such that they could assemble in a short amount of time. These things made them stand out from colonial militias that were not as well trained or mobile.
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