Tartakovsky, who created the animated series hits "Samurai Jack," "Dexter's Laboratory" and "Star Wars: The Clone Wars," will involve his Orphanage Animation Studios to take the lead on the CG animation elements for the puppet-driven film.
Brian Froud has returned to design the new characters.
The pic's development has so far been funded by Henson. Overseas distribution will be sold during the Berlin Film Festival by Odyssey Entertainment; Henson will secure a domestic distributor by the time the film begins production in late summer.
Annette Duffy and David Odell penned the script.
Set hundreds of years after the first pic, sequel follows a mysterious girl made of fire who steals a shard of the crystal in hopes of reigniting the dying sun.
"The original 'Dark Crystal' was the pinnacle of puppetry; they created characters that were as believable as the ones you see in animated films," Tartakovsky said. Tartakovsky said that unlike in the pricey original film, for which otherworldly sets were built, the puppets this time around will operate amid a CGI backdrop.
"There is a limited budget here, and this will be more artsy, in a "Sin City" fashion, with characters performing over greenscreen and great backgrounds behind it," he said.
Brian Henson, Ralph Kamp and Louise Goodsill will exec produce.