The women, identified according to their lawyers' initials as M.M., a 41-year-old born in Toronto, and J.H., a 61-year-old born in Ottawa, were married on June 18, 2003, one week after the Ontario Court of Appeal legalized same-sex marriage in the province.
The couple separated five days after the wedding, ending an almost 10-year relationship, J.H.'s lawyer Julie Hannaford said.
"This is the first same-sex divorce case in Canada to our knowledge," M.M.'s lawyer, Martha McCarthy, said in court documents.
The petition, filed in the Superior Court of Justice last month, was to be heard Sept. 13. It will add a new facet to the contentious legal debate over same-sex marriage. The Supreme Court of Canada is holding hearings on the legality of same-sex marriages in the fall.
The ruling Liberal government has vowed to legalize same-sex marriage across the country although polls have shown about half of Canadians are against the move.
So far, courts in Ontario, Quebec, British Columbia and the Yukon territory - overseeing some 70 percent of the country's 31 million people - have ruled that the right for gays and lesbians to marry is guaranteed by the Canadian constitution's Charter of Rights.
However, the federal Divorce Act hasn't been amended to apply to same-sex couples.
M.M. and her lawyer are asking the court to grant the divorce and declare the Divorce Act's definition of spouse unconstitutional. The divorce law defines a spouse as "a man or woman who are married to each other."
The government says it wants to go further and strike down the entire definition of spouse in the act.
M.M. said the couple have no possibility of reconciliation. They signed a separation agreement on April 30. Grounds for divorce in Canada are separation, adultery and cruelty.