Rafael Martinez is a Lieutenant at Boston Police Department in the Drug Unit.
Rafael Martinez was in the Drug Unit at BPD with Jane Rizzoli. They worked a cover together as a couple when out at clubs (drinking, dancing, etc.). At some point near the end of their time together as partners they got Jane's CI, Yolanda, killed. Rafael left for a Federal Task Force and was gone for 8 years until his return to be Lieutenant. He returns in Season 4 with an obvious and mutual dislike of Jane Rizzoli and is newly promoted Frankie Rizzoli's boss.
It is implied that Jane & Rafael were together in the "Biblical sense".