Molina, who recorded as Songs:Ohia and with the band Magnolia Electric Co. passed away on Saturday in his Indianapolis home, a spokeswoman from his record label wrote via e-mail.
Molina has been out of the public spotlight for a number of years due to health complications stemming from alcohol abuse.
His family issued an appeal to his fans in 2011 to help cover the musician's medical bills. "It has been a very trying time for Jason, his friends, and his family. Although no one can be sure what the future holds, we feel very encouraged by the recent steps Jason has taken on the road towards becoming healthy and productive once again," the family wrote.
Musician and writer Henry H. Owings wrote this tribute to Molina on his blog, Chunklet.
"Jason leaves behind him an enviable body of work that will be continually rediscovered because what Jason wrote wasn't fashion. It was his heart. It was his love. It was his demons. And ultimately, it brought his life to an end."
RIP Jason Molina. I profiled him for the Trib in 2006. The man loved Chicago, approached work as few songwriters did: http://t.co/a40Sm8e1oe
i'm so saddened by this. he was one of my faves. his voice will be missed. -- R.I.P. Jason Molina http://t.co/GCPPOtCCoM @TheAVClub
I'm crushed. Jason Molina dead at 39. What a tremendous talent and a grave loss.
Getting to interview the gracious Jason Molina was by far one of the best experiences of this stint in community journalism. #ripmolina
Here's my obit on #JasonMolina. I'm very sad right now. http://t.co/5FEERmZV5l #fb
RIP Jason Molina. Your music soothed me when I really needed it. Thanks for broadcasting such a beautiful voice.
R.I.P. Jason Molina and Matt Suhar. Both taken from us too soon. Will miss you both.
RIP, Jason Molina. Addiction is such a terrible thing. Jason Molina - It's Easier Now: http://t.co/wXxSgair3Y via @youtube
goddamn, Jason Molina is dead. may he find peace and understanding now - as much as we've found because of his music. http://t.co/mbHcyPrBcD
Songs: Ohia - Farewell Transmission
From the CD Magnolia Electric Co. The whole place is dark Every light on this side of the town Suddenly it all went down Now well all be brothers of the foss...
Magnolia Electric Co - "Hold on Magnolia"
Magnolia Electric Co performing "Hold on Magnolia" on We Have Signal.
Songs: Ohia - John Henry Split My Heart
From the CD Magnolia Electric Co I stood on the 66 Hwy Wysteria, Magnolia beside the green line track Said Dont Come Back I found myself standing on the moun...
Magnolia Electric Co. "Farewell Transmission" (SBD Audio)
Jason Molina & Magnolia Electric Co. circa 2003. Recorded at The Village Tavern Mt. Pleasant, SC 9.9.2003. Initially we had two cameras ready for the evening...