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 with tampering 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 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.
Jennifer Dulos still has not been located. Additional details on the arrest were not immediately available.
"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 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.