The Nigerian takes over the armband from Gudni Bergsson, who retired from playing at the end of the last campaign.
"It is a great honour to be captaining Bolton Wanderers. I have enjoyed playing in Bolton and I have a great commitment to this club," the midfielder told the official Wanderers website.
"I have been playing at the highest level for a long time and the experience that I can bring to the club in this new position will be good.
"I have captained my country on a number of occasions and I have always responded to that extra responsibility."
Bolton boss Sam Allardyce is confident the former Paris Saint Germain player is the right man for the job.
"I was impressed with the way he took on the extra responsibility towards the end of last season. On several occasions, he was world class.
"He showed great maturity when it was needed and his experience rubbed off on other players in the squad."
Allardyce added: "A good captain needs to be able to communicate with other members of the squad on various levels effectively. Jay Jay can converse with our multi-international squad in different languages and that is very important to us."
