The other man was identified as Prakash, convicted in a theft case.
The duo's escape was detected early this morning when jail officials went for a headcount and found the lock of their cells broken, prison officials said.
A special team has been formed to trace them, they said.
Jayanandan was sentenced to death in 2010 for murdering a 51-year old woman in October 2006.
He had twice been caught earlier while trying to escape from a prison in Kannur and from another jail in Thrissur district.
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