The St. Petersburg Times reported NiShea Gilbert filed for court protection after receiving a threatening message on her cell phone on May 2, as well as a text message that included a picture of a handgun.
The Devil Rays said they were aware Dukes' marriage was ending, but that the allegations detailed in the story caught the team by surprise.
Manager Joe Maddon said he made the decision to sit Dukes Wednesday night, although the young center fielder was in uniform and available to play if needed.
"It was my decision to not play him," Maddon said after he and Devil Rays executive vice president Andrew Friedman met with Dukes before the game.
"In visiting with him, I can see he's pretty much upset. I anticipated that, so I thought the wise thing to do would be to not start him tonight and more than likely play him tomorrow."
Dukes and his wife has been married since February 2006 and have two children, whose safety also were threatened in the phone message Gilbert played for the newspaper.
Gilbert also gave an account of an April 30 incident at the middle school
where she teaches, saying Dukes showed up at her classroom while her students were at lunch and threatened her.
Gilbert said she and a co-worker went to the school office for help.
"I told them to get the deputy because he was acting out of his mind," she told the newspaper. "I told them, `Just have him escorted off. I don't want him to go to jail. Just make him leave."
Team president Matt Silverman said the "allegations raised in the article were news to us."
Dukes has a history of problems on and off the field, including an arrest in January on a marijuana possession charge. A tumultuous season at Triple-A Durham in 2006 ended with him being suspended for the final 30 games.
The product of Tampa Hillsborough, the same high school that sent Dwight Gooden, Gary Sheffied, Vance Lovelace and Carl Everett to the majors, reported to spring training eager to leave his troubles behind.
He not only won a job, but made his big league debut on Opening Day at Yankee Stadium because regular center fielder Rocco Baldelli had a hamstring injury and was limited to a designated hitter role.
"He's made progress," Silverman said. "These allegations are troubling, but they are ones that we hope that he and his wife and family can work through and have him back on track as soon as possible."
Dukes' ability on the field has never been an issue, however his temper and several off-the-field transgressions have raised questions about whether he'll ever reach his full potential. Through Tuesday, he was batting .231 with eight home runs, tied with Cincinnati's Josh Hamilton for the most among major league rookies.
"We've been working with him closely and we have seen some improvement. We believe he has the potential to be a great ballplayer and be an outstanding citizen. And, we're committed to helping him reach his potential," Silverman said.
Maddon said he had not asked Dukes for his side of the story.
"I did not feel it was necessary for him to tell me anything more than what I read today. Maybe at some point. But for today, no," Maddon said.
"I'm just concerned in general, how he's going to handle things. We'll wait and see how it all shakes out. ... For today, I felt it was in his best
interest and our best interest to not start him."
Silverman said the Devil Rays had been in contact with Dukes' agent, as well as major league baseball.
Meanwhile, the club will continue to offer help through its confidential
employee assistance program.
"We've had a number of conversations with him," Silverman said. "The end of a marriage can often be a messy situation. Our focus is not on the different sides of the story but more ensuring Elijah has all the resources he needs to help him at this time."
Teammate Carl Crawford said he and other players were not familiar with any problem Dukes had at home.
"If he wants to talk about it, we'll talk. If not, it's one of those things
you kind of let play out and see what happens," Crawford said.
"For this to come out, it's kind of like a setback to him that he'll have to deal with. I don't think it's going to affect the clubhouse. That's personal stuff. I don't ask any player about their issues at home."
By: Tampa Bay rookie Elijah Dukes was held out of the lineup Wednesday night against Seattle following a published report that his estranged wife sought a restraining order after being threatened by the 22-year-old outfielder.