This is from wikipedia (https://en.wikipedia.org/wiki/Enrolled_Missouri_Militia):

" ... a compulsory militia enrollment was declared on July 22, 1862, the Enrolled Missouri Militia. Schofield issued General Orders No. 19 requiring loyal men to enroll in the militia, required registration of all who had previously taken up arms against the United States, and for them to surrender their weapons. The disloyal and Confederate sympathizers would not be required to enroll in the militia, but would have to declare their sympathies, which many were unwilling to do and instead enrolled."

Many pro-southerner Missourians did join the EMM, so many that the Provisional EMM was eventually instituted to be made up of vouched for pro-northern men. From wikipedia (https://en.wikipedia.org/wiki/Provisional_Enrolled_Missouri_Militia):

"The Provisional Enrolled Missouri Militia was created by Missouri Governor Hamilton Rowan Gamble in 1863 when it was determined that the mixed sympathy part-time Enrolled Missouri Militia was not an effective garrison force against guerrilla activity. Reliable Unionists were selected from the EMM regiments and the enrolled militia were disbanded."