The central issue of the 1866 congressional elections was President Johnson's reconstruction policy. The policy heavily favored the south and was extremely lax about the treatment of newly freed slaves. Republican members of Congress disagreed with the policy and refused to recognize it.
After the Civil War ended, the United States entered a period of rebuilding. Aside from the literal rebuilding of cities and towns that had suffered significant damage during battles, there were many lingering social challenges. Slaves were now free and needed to be integrated into society. Southern states that had seceded before the Civil War had to be re-initiated into the United States.
Northern Republican members of congress felt that there should be conditions for Southern states to meet before permitting them to rejoin the union. Johnson, however, was a southerner, and his policy for re-entry was very lenient, which angered congress. Johnson also did little to assist slaves in securing the freedom to which they were now legally entitled and integrate them into society. The tensions between the president and Republican members of congress grew so intense that Johnson embarked on a multi-state tour just weeks before the election of 1866 to campaign against the "radical" Republicans of congress.