Miguel Diaz Rivera was arrested late Friday in the Dominican capital of Santo Domingo. Puerto Rican police said Saturday he had been living there under a false identity.
The 39-year-old faces charges including murder and drug possession and is being held on a $1.2 million bond. He is accused of running a drug trafficking network in at least five Puerto Rican cities.
Diaz is expected to be extradited soon.
The U.S. Caribbean territory blames drug trafficking for the majority of its killings. More than 1,066 people have been killed this year on the island of 4 million people, a record number.