Police revealed the grim news at a press conference today when Detective Superintendent Reg Bevan said: "Mark Bridger has been arrested on suspicion of the murder of April Jones.
"He remains in custody at Aberystwyth police station, where he continues to be questioned.
"The arrest does not detract from our efforts to find April and we remain committed to finding her.
"Her family has been informed of this development and, as you would expect, they continue to be supported by a family liaison officer."
The arrest came amid reports that searchers were using sonar equipment to scour the River Dyfi, which has been one of the focal points of the hunt.
Superintendent Ian John acknowledged again that volunteer searchers had played a "vital part" in the hunt for April so far.
But the dynamic has changed with the announcement that Bridger is now being held on suspicion of murder, he said.
Searches will continue but the focus has inevitably changed from looking for a live child to one of looking for a body.
Bridger, 46, was arrested on Tuesday, a day after April disappeared while play-ing near her home in Machynlleth, west Wales.
April was seen willingly getting into what is believed to be a Land Rover Discovery on the Bryn-y-Gog estate at 7pm on Monday.
Bridger, from Machynlleth, drives a Land Rover Discovery which was seized from a local repair garage on Tuesday and fast-tracked for forensic examination.
Detectives have until this afternoon to question him – unless they apply for a further warrant of detention.
Superintendent Ian John said that because of today's "significant development" it was no longer appropriate for the many volunteers who had joined the hunt for April to continue searching.
He said: "You have heard about a significant development in this investigation, which has an impact on our search.
"We want to acknowledge and are extremely grateful for the efforts of the community volunteers who have supported the professional searchers in trying to locate April.
"They have been a vital part of our team throughout this search operation. Quite frankly, their commitment has been an inspiration to us all.
"The dynamics of the search have now changed and, due to the passage of time and the developments within the investigation, it is no longer appropriate for us to expect untrained members of the public to continue the search.
"So now we require only professional searchers to be involved in the search that continues in and around Machynlleth.
The brief press conference in Aberystwyth today was in stark contrast to the upbeat approach of many residents yesterday.
In response to an appeal from mother Coral Jones to "wear a pink ribbon for April", residents had acted quickly to show their solidarity.
Today, Mr Bevan spoke only briefly to reveal the dramatic development. Looking tired and drawn himself on the fifth day of searching, he renewed the appeal for information about Bridger's movements.
The sombre mood at the press conference was mirrored among members of the media present to report on the case.
Both officers left the room in silence instead of waving away the usual questions from reporters for more information.