A major concern of Congress at the time of the Missouri Compromise was maintaining a balance between the free states in the North and the slave-holding states of the South. The two sections of the country had thus far kept a balance; there was a similar number of states on either side, and the North's growing population was offset by an earlier compromise in the Constitution allowing slave states to count their slaves as 3/5 of a person for the purposes of population-based representation in the House of Representatives.
The proposed admission of Missouri threatened that balance, as the territory contained many settlers from the South who had brought their slaves with them. An attempt to admit Missouri as a free state failed, but in 1820, Jesse Thomas of Illinois proposed to admit both Missouri (as a slave state) and Maine (as a free state) simultaneously, with the additional condition that slavery would not be allowed to spread north of the latitude 36º30', which was Missouri's southern boundary.
This compromise kept the peace for a while, but the issue of slavery would eventually ignite the Civil War just thirty years later.