1530s, "different, at variance, disagreeing," from Latin dissidentem (nominative dissidens), present participle of dissidere "to be remote; disagree, be removed from," literally "to sit apart," from dis- "apart" (see dis-) + sedere "to sit," from PIE root *sed- (1) "to sit."
Meaning "dissenting, not conforming" is from 1837, originally in reference to an established church. Meaning "disagreeing in political matters" is by 1943.
"one who differs or dissents from others," 1766, in reference to Protestants and other non-Catholics in Poland, from dissident (adj.). General sense of "an opponent or non-conformist with regard to a prevailing opinion, method, etc." is by 1790, at first especially with reference to religion. In the political sense it is used by 1940, coinciding with the rise of 20c. totalitarian systems, especially with reference to the Soviet Union.