The girlfriend of Fotis Dulos, Michelle Troconis, 44, has also been arrested, according to a press release by the New Caanan Police Department. They were both charged with tampering with or fabricating physical evidence.
The couple was taken into custody on Saturday in Avon, Connecticut, police said. They are being held on $500,000 bond each and are scheduled to appear in court Monday morning.
Jennifer Dulos, 50, was last seen on May 24 in New Caanan, Connecticut, driving a black Chevrolet Suburban. She was last heard from while dropping off her children at school that day, police said.
Her vehicle was later found near Waveny Park in New Canaan, police said.
According to a letter from Fotis Dulos' attorney on Tuesday, her nanny brought the couple's five children to Jennifer Dulos' mother's home, where an armed bodyguard was hired to watch them.
It is unclear where the children are currently, but a statement from family spokeswoman Carrie Luft on Friday said they are "safe and well-cared for."
Fotis Dulos, 51, and Jennifer Dulos have been embattled in a divorce since 2017, court documents show. They married in 2004.
In 2017, Jennifer Dulos filed for an emergency order for full custody of the children, which was denied, court documents show. Jennifer Dulos and Fotis Dulos had temporary shared custody of the children until the end of the divorce proceedings.
In the order, Jennifer Dulos stated that they discussed separating after she learned of her husband's affair in March 2017.
Jennifer Dulos alleged that Fotis Dulos exhibited intensifying "irrational, unsafe, bullying, threatening and controlling behavior," stating that she was afraid for her safety as well as the physical safety and emotional well-being of their children.
The mother alleged that Fotis Dulos threatened to kidnap their children on May 30, 2017, if she did not agree to his terms in the divorce settlement and that he had bought a gun that year.
Jennifer Dulos described an incident on June 3, 2017, in which Fotis Dulos allegedly became enraged over her scheduled activities for their children on a Saturday morning because he felt that they should be waterskiing instead. Jennifer Dulos claimed that her husband would force the children to train as professional waterskiiers, even though they did not want to, but they were "all afraid to disobey," she stated.
"He got within inches of my face and berated me" the court documents state. "I was scared and tried to leave the room. He followed me upstairs and into a bedroom, where he shut the door and blocked it so that I was trapped as he verbally attacked me and physically intimidated me."
The couple's daughter and babysitter were allegedly in the room at the time and witnessed Fotis Dulos blocking the door, according to the court documents.
"Having no way to escape the room other than a second story window, I screamed until my Husband became nervous that his cousins, who were visiting the home, would hear me," the emergency order states.
In the request for relief, Jennifer Dulos stated that she knew that filing for divorce and filing the emergency motion for custody would "enrage him."
"I know he will retaliate by trying to harm me in some way," she said. "He has the attitude that he must always win at all costs. He is dangerous and ruthless when he believes that he has been wronged."
In Fotis Dulos' amended reply to the motion, he claims that he legally bought the gun in 2017 for home security and stated he never threatened or bullied the children into waterskiing, court documents show. He denied exhibiting "irrational, unsafe, bullying, threatening and/or controlling behavior" and stated that he never threatened to kidnap the children or physically threatened his wife.
In an email to Jennifer Dulos in December 2017, Fotis Dulos wrote that their children "deserve a mother AND a father, not one or the other."
"And if we cannot live together, we can at least get along for their sake and benefit," Fotis Dulos wrote.
Fotis Dulos claimed that in June 2017, his wife lied about where she was taking the kids and instead hired armed bodyguards and took them to a hotel in New York City. He claimed his wife told the children that "Dad" was "going to harm them," according to court documents.
Fotis Dulos also stated that his wife called him a psychopath and told the children that he does not care about them. In addition, Fotis Dulos claimed that his wife said to the children, "I will make sure this divorce takes two and a half years," and "I can have the Mafia break your dad's legs with a baseball bat."
After they separated, Jennifer Dulos and the children moved out of their home in Farmington, Connecticut, where Fotis Dulos remained, the Connecticut Post reported. Fotis Dulos operates his construction business, The Fore Group, out of the home, according to the newspaper.
Jennifer Dulos still has not been located.
"We miss her beyond measure — her five young children, her family, her friends, colleagues and neighbors, as well as countless people who have never met her but who have responded to the spirit of grace and kindness that Jennifer embodies," Luft said in the statement. "The support and love, the concern for her children and the community efforts to help locate Jennifer have kept us going."
ABC News could not immediately reach attorneys for Fotis Dulos and Michelle Troconis.
ABC News' Emily Shapiro contributed to this report.