The incident happened Friday night on a southbound C train platform at West 155th Street, where police say the couple harassed the 26-year-old victim.
Authorities say the man asked her if she was a man and then slapped her in the face and spit on her. The woman then allegedly slapped the victim's phone out of her hand.
Pablo Valle, 27, was reportedly taken into custody in New Jersey and will be extradited. Charges are pending.
Authorities say he has 27 prior arrests.
The female suspect has still not been located.
The victim, Serena Daniari, was not seriously hurt. But she immediately took to Twitter after the incident.
"I just wish people would leave me alone," she said in a video posted to social media. "I didn't do anything. I just want to be left alone."
Mayor Bill de Blasio responded to the tweet from the victim, apologizing to her on behalf of the city and adding that transgender and non-binary New Yorkers deserve to travel in their city without fear.
.@NYPDHateCrimes is investigating this loathsome, transphobic attack. If you have ANY information please contact them IMMEDIATELY.— Mayor Bill de Blasio (@NYCMayor) January 26, 2020
Serena, on behalf of your city I’m so sorry this happened. Transgender and non-binary New Yorkers deserve to travel in their city without fear. https://t.co/mLM46e6a7u
Gov. Andrew Cuomo directed the New York State Police Hate Crimes Task Force to assist the NYPD with its investigation.
"No one should ever have to live in fear simply for being who they are," Cuomo said. "New Yorkers embrace diversity and our differences, because that's what makes us unique and that's what makes us great. On behalf of the New York family, my message to Serena Daniari is simple: We have zero tolerance for what happened to you. We are sorry for what happened to you. We stand with you in love and respect, and we will catch your attackers and bring them to justice."
The victim released a statement later Sunday thanking everyone for their support but asking to respect her privacy as she moves forward.
Anyone with information in regard to this incident is asked to call the NYPD's Crime Stoppers Hotline at 1-800-577-TIPS (8477) or for Spanish, 1-888-57-PISTA (74782).
In response to this incident and others like it that have led to a 42% increase in hate crimes in the transit system, the MTA announced Monday it is launching a new "Hate Has No Place in Our Transportation System" public awareness campaign.
"New York is built on diversity, openness and inclusion," MTA President and CEO Patric Foye said. "Every New Yorker should be able to travel free of harassment and feel safe while riding with the MTA. We want to do what we can to put a halt to these despicable crimes. We hope that our campaign will not only help reduce bias activity but will remind everyone of the core New York values of kindness, respect and solidarity."
The ads will appear on more than more than 4,000 digital screens across the subway system, 2,600 screens on buses, and 550 screens on the Long Island Rail Road and Metro-North Railroad.
All ads feature iconic signage associated with the NYC Transit system, LIRR and Metro-North and share the message that "hate has no place" in the MTA network. The ads provide information on how to report hate crimes, concluding with the tagline: "New York rides together."
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