Matisyahu has two memories of Charleston. One was in the fall of 1996, when he made a pilgrimage to the North Charleston Coliseum to see Phish. Then 17 years old and a diehard Phish-head, he remembers driving around town afterward and being spooked by some rough neighborhoods.

His second memory is from the fall of 2009, when he returned as a major-label reggae-rock artist to play a show at the Music Farm. By then, he and his band had performed at Bonnaroo with Phish, and their own live show tended toward extended jams.

After the Music Farm set, he and a friend strolled through downtown. “We were taking a walk through a park and reviewing some ideas of Jewish mysticism,” Matisyahu says. “I remember the show was hot, and it was a young crowd.”

In conversation, Matisyahu shifts effortlessly from discussions about beat-boxing technique to postulations about the Infinite. “Someone was asking yesterday, ‘Do you see music as entertainment or always with deeper meaning?'” he says. In his mind, the two are not mutually exclusive.

Born Matthew Paul Miller, Matisyahu was brought up in Hebrew schools in White Plains, N.Y., where he picked up the Hebrew moniker that is roughly equivalent to the English Matthew. After the Phish years, he reconnected with the faith of his forefathers, spending several years in the Chabad-Lubavitch orthodox community of Crown Heights, Brooklyn.

“Crown Heights burnin’ up all through the twilight,” he rapped on his 2006 breakout radio hit “King Without a Crown,” splitting the difference between New York nasality and Jamaican affectation. “Said ‘I thank you’ to my God, now I finally got it right/And I’ll fight with all of my heart and all of my soul and all of my might.”

There is often a buoyancy to his music, both in the sunny instrumentals and in the ceaselessly optimistic lyrics. But his most recent studio album, 2009’s Light, finds him wrestling with darker questions and heavier subject matter than on 2006’s Youth. On the song “Escape,” he sings, “Lost my mind on the train running from the insane/Children taught to blow their brains out in the holy name/Running for fame where everybody knows your name.” And where Youth included paeans to, well, youth, Light has meditations on death and aging, including the song “On Nature.”

“It’s about being made of the elements of the world as opposed to being separate or alien to this world,” he says. “You’re made of the same material base as this world, so your body and somehow your soul are made of the same material as this earth, just sand, just rock, dry land.”

Matisyahu’s live concerts, too, have become leaner, more planned meditations. His new backing band, Dub Trio, takes a different approach than his old band, which he says “was all about trying to explore the musical space.” There are still some solos and improvisations, but they no longer dominate the show.

Sometimes, a song is a prayer. That was often the case in his early days as a musician, as on “Got No Water,” the second song he ever wrote, whose refrain is a quotation from the Torah: “Shma Y’sroel, Hashem Elokainu, Hashem Echad” (“Hear, Israel, the Lord is our God, the Lord is one.”)

Matisyahu’s newly released concert album Live at Stubb’s Vol. II — recorded at the famed Austin, Texas, venue last August with the Dub Trio — is his first offering since Light.

“I think the whole concept of prayer is reaching outside of yourself,” he says. “In some ways, when you’re doing music, you have to reach into yourself. It’s a little bit different, but it all comes down to being in that moment. If you can be in the moment in the music and you can be in the moment when you’re speaking to God … I think that’s where it’s at.”

Theological treatises aside, Light is a triumph of fusion. Slickly produced reggae transitions seamlessly into a sound that actually gives the rap-rock genre a few ounces of respectability. At the center of it all, Matisyahu raps with all the bravado of a dancehall toaster and beat-boxes with spittle-flinging intensity. He treats his voice as a musical instrument and music as a sacred form of communication.

“It is the expression of the thing that is the most intimate and the most holy and the most beautiful that lies within us,” he says. “I guess that’s the idea. It’s on a level that’s way, way beyond. It bypasses the mind, bypasses the intellect, and it just goes straight for the heart.”

Spoken like a true Phish-head.