Eight plainclothes RCMP officers arrested Winston Blackmore, 52, and James Oler, 44, Wednesday in the town of Bountiful, The Province newspaper in Vancouver reported.
The two are rival leaders of the Fundamentalist Church of Jesus Christ of Latter Day Saints, the Globe and Mail said.
Blackmore is charged with 19 counts of "practicing a form of polygamy or practicing a kind of conjugal union." Oler faces two similar charges.
The provincial government has been pushing for charges for several years, but there was legal dissent that charges would contravene Canada's Charter of Rights and Freedoms that guarantees freedom of religion, the reports said.
However, special prosecutor Terrence Roberts spent seven months assessing the case, and the decision to prosecute was ordered by the provincial attorney general, the Globe and Mail said.