Jones has been at Llanelli since 1998, scoring 83 tries in 155 games
Wales wing Mark Jones will be the Scarlets skipper for 2009/10, with Australian David Lyons as vice-captain.
Last year's skipper Simon Easterby and deputy Stephen Jones should continue to play key roles at the region.
Builth Wells-man Jones, 29, has played 155 games in 11 years with Llanelli and the Scarlets, scoring 83 tries, and has won 47 Wales caps with 13 tries.
"Mark and David will bring a lot to the leadership of this new-look team," said Scarlets coach Nigel Davies.
"We're really grateful to Simon Easterby and Stephen Jones for what they have done as captain and vice-captain and - as two of our most experienced Scarlets players - these will be big boots to fill.
"Like Simon, Mark Jones embodies everything that the Scarlets stand for.
"In addition to his talent and experience on the field, he has shown he has great pride and belief in the region's values and its playing ethos.
"David has had a major impact on this side from the very beginning and his commitment and professionalism has been an example to all.
"He has a wealth of experience and this new responsibility will give him more scope to help develop talent within our squad."
The new skipper, a Grand Slam winner with Wales in 2008, expects better from the Scarlets after last season's disappointments.
I'm looking forward to a bit of time off after the Lions tour and then joining back up with my Scarlets colleagues
Scarlets, Wales and Lions fly-half Stephen Jones
"We've been through a challenging time and last season was plagued by injuries, but this season brings a fresh start and there's an upbeat mood in the camp since we returned for pre-season," Jones told the Scarlets' website.
"Going forward I think we have a lot to be positive about, some of the younger guys have shown what they're capable of and we have a strong group of very experienced senior players who will have more of a role next season in helping take things forward."
Lions fly-half Stephen Jones, back on home soil after his exertions in South Africa, welcomed the new regime at Parc y Scarlets.
"Mark is a true Scarlet and obviously I have known him for quite a while," said Jones, who was on the field for the entire three-match Test series against the Springboks.
"He has proved himself as a great player on both the regional and international stage and will be a popular captain with team mates and our supporters."
Lyons, 29, has 43 Wallabies caps to his name and joined the Scarlets on a four-year deal last summer, going on to play in every competitive game for the region in 2008/9.
"There's no doubt David is a very intelligent rugby player and will pass on a lot of his experience and motivation to the younger group of players that are coming through," said Stephen Jones.
"I'm looking forward to a bit of time off after the Lions tour and then joining back up with my Scarlets colleagues."