PHILADELPHIA—Five minutes after the last out of the Phillies 14-2 loss to the Miami Marlins at Citizens Bank Park today, Roy Halladay was – to the organization’s knowledge – healthy.

Five minutes later, that knowledge changed.

Phillies GM Ruben Amaro said after the game Sunday that Halladay is likely headed to the DL with what his 35-year-old righthander called “discomfort” in his throwing shoulder.

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“He’s experiencing some shoulder difficulty, some shoulder pain. We’re likely going to have to put him on the DL,” Amaro said.

The Marlins erupted on Halladay on Sunday for nine runs through only 2 1/3 innings on Sunday, his first start after being blasted for eight runs in 3 2/3 last Tuesday in Cleveland, making for only the second set of back-to-back starts of eight runs or more for Halladay and first since May 2007.

That week six years ago, Halladay underwent appendectomy surgery.

Now, the Phillies aren't sure what the problem is.

Halladay will meet with Dr. Lewis Yocum in Los Angeles while the rest of the team heads to San Francisco and Arizona on their first West Coast trip this season. Preliminary tests were conducted after the game by team physician Dr. Michael G. Ciccotti, and were inconclusive.

“Until we do any diagnostic work, we won’t know exactly what’s going on with him,” Amaro said. “But clearly he doesn’t seem like he’s healthy. Pretty apparent with his performance today, unfortunately.”

Halladay said he first felt the pain the morning after his start against the Pittsburgh Pirates on Apr. 24, when he dealt six innings of one run ball in a 5-3 team loss.

“Woke up, didn’t really think anything of it,” Halladay said. “Was kind of regular soreness. Just kind of progressed over the last two weeks or so.”

Halladay said he believes the issue to be something new, and unrelated to the right shoulder and lower back problems that led to a seven-week DL stint last summer.

“It’s not something that I’ve had before,” Halladay said. “It’s something new this year. I felt good all spring, felt good all year. Just kind of got up after that start against Pittsburgh and had soreness in there and wasn’t able to get rid of it.”

Amaro said the organization had not been alerted of Halladay’s condition until today.

“He hasn’t been on our injury report for any discomfort,” Amaro said. “Now he is. Now he will be.”

Manager Charlie Manuel took the podium postgame with the belief Halladay was still healthy.

“We always check,” Manuel said when asked if Halladay was hurt. “After every start, as a matter of fact. We do with all our pitchers. That’s kinda how it goes. Plus, he just pitched today, we haven’t talked about his pitching yet. I gotta come in here and talk to you guys before I do anything.”

Sunday’s development marks the latest wrinkle in and up and down and all over 2013 for Halladay.

After being blasted for 12 runs in 7 1/3 innings in his first two starts this season, Halladay worked a three-game stretch of 1.71 ERA ball – the last of them being his start against the Pirates.

In two starts since, against the Marlins today and Indians last Tuesday, Halladay’s ERA is 25.50.

Amaro has yet to make an official move, and said he must first decide who will replace Halladay in the rotation. Adam Morgan, the Phillies prized 23-year-old pitching prospect, went today for Triple-A Lehigh Valley and so would be available for Halladay’s next scheduled turn on normal rest.

But the general manager said the likely outcome is another trip to the DL for his $20 million pitcher.

“Pretty certain,” he said. “We have to figure out what we’re going to do with our roster and who’s going to be pitching. But we think it’s fairly certain.”

Amaro addressed the fact that Halladay did not right away inform the team of his condition.

“He’s a competitor,” Amaro said. “If he feels like he can pitch, he’s going to pitch, and we’re going to let him pitch. But clearly he wasn’t able to pitch to his accustomed level, and it was apparent today and after his last outing.”

He was also asked whether he was relieved to be able to pin his ineffectiveness to an injury.

“I don’t think any of it’s good news when one of your very important players is hurt,” he said.