The 4-year-old dog was not wearing a collar when it got on the bus early Wednesday morning and made herself comfortable on one of the benches, the New York Daily News said.
The bus operator contacted police, who brought the dog to Staten Island's animal shelter.
A microchip was embedded under the dog's fur, but didn't have any information on it because it was never registered, the Daily News said.
But an animal rescuer contacted the manufacturer of the chip and discovered Michael Kanaskie, of Hollywood, Fla., purchased the device more than two years ago.
Kanaskie said he had given up looking for the dog, named Marly, after his former spouse gave her away without his permission.
"My birthday is tomorrow," Kanaskie said. "This is the greatest gift for my birthday."