Rohan Marley didn't abandon her while she was pregnant, and he's not the baby's father, the singer has said.
The blogosphere has been abuzz after news came last week that the Grammy winner had a baby boy.
Rohan, the father of her five other children, sent a message on Twitter "forwarding all well wishes to Ms Hill on the birth of her new son".
That tweet, along with pictures showing him in an embrace with another woman, created speculation.
Lauryn has rarely discussed their long-term relationship.
She posted a message on Twitter and her website defending Rohan, her partner of 15 years.
The 36-year-old singer said they've had a "long and complex history" but love their five children together.
Although never married, the couple are parents to Zion, 14, Selah, 13, Joshua, 9, John, eight and three-year-old Sarah.
Thirty-nine-year-old Rohan - the son of late reggae lengend Bob Marley – was not at the birth of Lauren's little boy.
Mystery still surrounds the identity of the new arrival's father.
When it became known in June that the singer was pregnant, Rohan had hinted the baby was not his.
Speaking to a Houston Chronicle reporter during a conversation on Twitter, Rohan said: "I'm not married and I don't have anyone expecting anything."
The journalist then responded: "So we are clear. 1. You're not married to your ex-wife or Lauryn, and 2. She isn't preggo w/your child, but someone else's?"
"That is correct until I say out of my mouth to the contrary," Rohan confirmed.
Lauryn got together with Rohan – founder of organic coffee company Marley Coffee – in the summer of 1996.
At the time he was still with his wife Geraldine Khawly.