Civil marriage equality cannot legally be denied at the territory level, via the Supreme Court of the United States, as of 26 June 2015.
On 26 June 2015, the Supreme Court of the United States (SCOTUS) ruled FOR marriage equality and that same-gender couples have the constitutional right to marry in all 50 states and all U.S. territories.
Same-sex marriage became illegal on 19 March 1999, when H.B. 1013 was signed into law. The law defined marriage as "a civil contract whereby a man and a woman mutually agree to become husband and wife."
Pedro Rossello, the former governor of Puerto Rico and a staunch conservative, who, when he was in office, signed the law that prohibited same-sex couples in PR from marrying, publicly expressed his unconditional support for same-sex marriage in February 2013.
Following the 2013 SCOTUS ruling in United States v. Windsor, both the IRS and the Department of Labor (DOL) wrote that for their purposes the term "spouse" refers to any individual who is lawfully married under any state law, including individuals married to a person of the same sex who were legally married in a state that recognizes such marriages, but who are domiciled in a state that does not recognize such marriages. This applies to Puerto Rico.
Current Governor Alejandro Garcia Padilla is pro-LGBTQ rights. Gov. Padilla signed a bill that bans employment discrimination based on gender or sexual orientation, and he included same-sex couples in a domestic-violence law.