Lochan and Misty, who are both believed to be 37 years old, have not been seen since last summer.
Dave Sexton, RSPB officer for Mull, said he is certain the eagles, who had 39 chicks over the years, are dead.
He said: “They are not going to move to a new area at their age and I would have seen them if they were still here.
“All the evidence leads to their demise.”
It is believed that the birds may have been attacked by a new pair of sea eagles which have taken over their old nest in the Loch Don area of the island.
Mr Sexton said: “A new pair have moved in and there has been lots of aggressive chasing between the two pairs.”
No dead eagles have been found on Mull but one white- tailed sea eagle was recently found dead on the mainland, directly across from the island.
Mr Sexton said: “We haven’t been able to do any DNA on it to find out if it is definitely one of the old eagles.
“It looks like it’s the end of an era. Misty and Lochan starred in Blue Peter and Springwatch.
“They were the first eagles to build a nest on Mull, the first to lay eggs, although they weren’t successful with chicks until 1986.
“Since then they have been an amazingly productive pair, who helped us establish the white-tailed sea eagle population.”
The old eagles were originally from Norway and were released on the Isle of Rum National Nature Reserve as part of the Scottish sea eagle reintroduction project, which began in 1975. There are now 20 pairs of sea eagles on Mull and, as fears grow for Lochan and Misty, there is good news at the Mull eagle watch hide, where two chicks have just been born.
Male eagle Star and female Hope were seen at their nest with the new chicks on Tuesday.
Mr Sexton said: “They are about a week old now.
“Mull and Iona Community Trust ranger Rachel French has seen them and I have seen them. Rachel got a photo of the chicks with Hope.
“There is sad news about Misty and Lochan but there is good news that the next generation have hatched successfully.”